1. Jim just...abandons Karen in NYC to ask out Pam?
The ongoing will-they-won't-they flirtation of Jim and Pam is handled incredibly well for the first few seasons - they're compelling and obviously belong together and that kind of office crush scenario is really rarely shown in any kind of TV show as well as it is in The Office. But then something comes along to crash the whole thing: Karen Filipelli.
And here's the real problem - Karen's great. While Pam and Jim had obvious chemistry, Pam chose to stay with Roy and not pursue Jim over and over again. When Jim took a leap and kissed her, she told him she couldn't do this. Jim took a risk, and she rebuffed him - which is fair, since she was engaged at the time and the relationship already had a huge amount of baggage. But then Karen shows up - and she is FREE of baggage. She likes Jim and she's honest and upfront with him right out the gate. She's fun and kind and smart - all the things Pam is, but without any of the weird baggage.
But, obviously, Pam and Jim were always going to end up together, so the writers figured they would stop beating around the bush and get them in a relationship...but they had to throw Karen under the bus to do so. Well, almost that. Jim and Karen were in New York to interview for a position at corporate when Jim realized that it was truly Pam that he wanted to be with - and so he drives back to Scranton to ask her out!
...and abandoned his current girlfriend in New York City. While she was out getting lunch with some friends. And with no way of getting back to her home in Scranton, since Jim was her ride. So - what was supposed to be a grand romantic gesture ended up being a total dick move.
Which leads to the next issue...
2. Jim and Pam suck together
The relationship that started on the rockiest foundation possible (a dude abandoning his current GF in another state and leaving her stranded with no ride home) wound up being pretty boring and shitty - who would've guessed!
The fun of Jim and Pam's relationship in the first three seasons was the tension - they both clearly had great chemistry together, but they could never consummate anything because obstacles kept getting in the way. It was a flirtation with real stakes and problems - and once they get together, their relationship is...well, just too nice.
There is really nothing less compelling in the world of sitcoms (or, really, any form of storytelling) than a pleasant, happy couple. Successful relationships are all about compromise and building up the coupling at the expense of your individual independence. In other words - characters you like lose their edge, and become something terrible: super boring.
Jim and Pam from The Office are the prime example - once they get together, they're (mostly) happy throughout the rest of the series, and as a result, both become instantly less interesting characters. They talk through their problems, they make time for one another, and both of their lives are immeasurably better - at the cost of the entertainment of the show plummeting. If only they had stayed apart and semi-miserable for all 9 seasons, everything would have been so much better (for us, not them).
3. Jim's pranks go too far
Here's the thing: Dwight's a dick. He really, truly is. He's weird, pretentious, and just generally annoying. So to put him in his place, Jim's taken up the habit of pranking Dwight lots and lots - many of which are the show's best gags (Asian Jim is probably the best). But while some of the pranks are nice, harmless fun, sometimes Jim's pranks are just kinda mean-spirited.
Not all of his pranks, for sure - stuff like Asian Jim and convincing him that he wa turning into a vampire are passive and depend a lot on Dwight behaving in a specific way where he's not actually embarrassed or hurt purely because of Jim's actions. But some of the pranks - like moving Dwight's desk into the bathroom, putting his belongings into the candy machine, and dressing up as Dwight are just kinda mean things to do without any provocation. Pranks are okay, but when you mess with someone's shit or just actively mock them to their faces in front of all your co-workers, that's pushing it a little far for a character who's supposed to be a sympathetic protagonist.
That being said, let us never forget Asian Jim:
4. Michael is TOO mean to Toby
Speaking of main characters being overly mean, there's a real problem with Michael being so unrelentingly mean towards Toby Flenderson. It's basically the Meg on Family Guy situation, where one character exists almost entirely to get dumped on nonstop - with the key difference being Family Guy is an absurdist cartoon where all the main characters are mean and terrible, and The Office ostensibly exists in the real world and usually asks us to feel bad for Michael and sympathize with his plight. And usually the show does a good job of portraying Michael as sort've an overgrown child - who can be mean and petty but also naive and kind. But when he's as mean as he is to Toby and never receives any comeuppance or consequences for it, it becomes less funny and more sad.
When Michael's mean to Pam or Dwight or almost any other character, he gets rebuffed or realizes he's wrong or embarrassed in some way, but pretty much never with Toby.
5. Threat Level Midnight sucks (because it's too good)
In an early episode of The Office, Jim and Pam discover Michael's secret screenplay - Threat Level Midnight, an action-thriller about a secret agent named Agent Michael Scarn and his pals Catherine Zeta Jones and Samuel L. Chang (aka "Dwigt"). It's a funny one-off joke that occasionally gets referenced later on - but in Michael's final season, the show actually shows the completed version of the movie Michael made over the course of several years.
And here's the problem: it sucks. But not like in the way it sucks because it's poorly written or dumb or whatever - it sucks because it's WAY too well-shot and looks really professionally done. Part of the great comedy of The Office (and of any of Michael's films, aka Great Scott Productions) is how the show understands the characters and how they could realistically get anything accomplished. Stuff like "Lazy Scranton" and Michael's presentation to new CFO David Wallace are perfect - mildly shitty in terms of quality, but clear Michael tried to spend time editing them and making them look as good as his abilities would allow (aka not too much).
But Threat Level Midnight just looks...great. It looks like it had a Director of Photography and professional cameras and lighting and everything. And that drains away the comedy, because it's clear that Michael Scott simply is not capable of producing something like this.
6. It makes no sense to promote Andy to manager
Let's be clear: we all know Andy got promoted to Manager in season 8 (post-Steve Carell era) because he played by Ed Helms, and Ed Helms had just gotten way famous for starring in The Hangover movies (which were actually really popular, even though they feel like they came out a million years ago). The network wanted to really show off that they had a big movie star on their channel, and so Andy became manager (and weirdly into a poor man's Michael Scott, but that's almost besides the point). The weird thing is....it really didn't make any sense for Andy to become Manager.
The whole nature of doing an American Idol style audition of tons of people by a committee (of Gabe, Jim, and Toby) was weird to begin with - Jim was technically the "number two" guy in The Office and should have been promoted straight away without question. And if he were to turn down that offer, it should definitely go to Dwight (who had seniority and was the best salesman in the company for multiple years running - the same reason Michael had been promoted to Manager). And yet they go with James Spader (aka Robert California) - an outsider who gave a real weird interview, who somehow becomes CEO on the first day and appoints Andy as Manager because he's "uncomplicated" and an "underdog" who people flocked to (neither of which were ever really true - he's got severe anger issues and deep-seated insecurities and no one really ever liked him or rallied behind him except Erin).
7. Pam becomes the saddest character on the show
Everyone finds a good deal of personal and professional fulfillment in the show - Michael gets the family he's always wanted, Dwight gets to be manager and married to Angela, Jim marries Pam and gets a job he actually WANTS to try at, and Pam....well, Pam gets Jim.
Of the characters on the show, Pam is really the only one who is ever shown to have a real passion for art. She loves drawing and sketching and design - and even if she may not be the best at it (Oscar and Gil give a pretty brutal assessment of her work as "hotel art"), it's something she loves to do. But...nothing ever comes of it, and she just ends up giving it up.
And that's somewhat true to life - our hobbies and passions are usually overrun by obligations to work and family and life in general, but this is a frickin' TV show where EVERYONE gets their dream except Pam. It starts in season 5, where Pam gives up really making a go at art school in NYC because it takes her too far away from Jim, and from there it just slips away further and further. She keeps making sacrifices of her own life for Jim's personal fulfillment (culminating in agreeing to move to Austin for Jim's dream job) after a whole season of Jim lying to Pam and ignoring her to build up his career.
And it's a shame, because - in the immortal words of Roy - her art was the prettiest art of all the art.
8. SCOTTS. TOTS.
The Office's bread 'n butter was always the cringe comedy of people acting in ways they should not, the reactions from normal people witnessing this awful behavior, and the stunned uncomfortable silences that surrounded Michael's blissfully ignorant inappropriateness. And while it NEARLY hit its peak with Season 4's Dinner Party, the writers went the furthest they could possibly go with Season 6's Scott's Tots.
In case you've repressed it in your memory, Scott's Tots involves Michael having to finally face up to a horrible promise he'd made to a group of underprivileged school children a decade earlier: that he would pay for all of their college educations. Michael did it at the time because he wanted to feel good and be praised - and assumed he'd have all the money in the world in ten years, never really understanding the reality of what his promise actually meant.
And when that reality came knocking at his door, he was forced to admit there was no way he would be able to pay for ANY of the kids' educations and that they'd pinned their hopes for their future to a lie for the past 10 years, and it is maybe the most emotionally brutal, gut-wrenching sequence ever aired on television. It's a work of art, but one that I don't think I can ever really stand to watch again.