1. Frank and Claire Underwood Have an Out-of-Nowhere Threeway with Their Secret Service Guy (House of Cards)
House of Cards is about 70% Frank Underwood convincing others to do really stupid, nonsensical things in order to fuck themselves over and 20% bizarre sex scenes (and 10% Doug Stamper being creepy for no real reason), but the big winner of the "okay what is even happening here?" sex award goes to Frank and his wife Claire inexplicably having sex with their secret serviceman, Meacham, at the close of an episode.
The weird part really isn't the actual sex - Claire 'n Frank are understood to use sex as a tool for establishing power over others, and have a relatively open relationship - but the fact that it's really given no introduction and basically zero followup makes it stand out as the writers just saying "We need something interesting to close out this random episode - why don't they just have sex with Meacham?"
It stood out enough that - even though pretty much everyone watched this season binge-style over the course of a single weekend - this was the one moment in a 13 hour block of TV that really stood out.
2. Buffy and Spike Bone a House To Rubble (Buffy The Vampire Slayer)
Buffy has its fair share of disconcerting sex scenes - from Buffy's sex with Angel causing him to turn into a soulless demon to magic lesbian witch sex - but nothing was weirder than Spike and Buffy starting a destructive relationship with one another, ever so subtly communicated by having them have sex so hard that it DEMOLISHES A HOUSE.
3. Gabourey Sidibe Had Sex With An Actual Minotaur (American Horror Story)
In case you're not familiar with American Horror Story, it's an anthology horror series where the plots don't make much sense, Jessica Lange plays a lot of different roles, and you will be subjected to an unsettling sex scene at least once per episode - which makes it difficult to choose ONLY ONE sex scene that's the most upsetting. Honestly, this list could be 90% AHS (without even getting to Hotel, the Lady Gaga season).
So, let's just go with the time Precious had sex with a minotaur. I'd give you more context, but that might just make things EVEN MORE confusing.