Some people hate Clint because they feel in all interactions, especially regarding Emily, he gives off the "Nice guy" vibe and he's all kinds of red flags.

A lot of it comes down to a single poorly written interaction. At some point (I think 8 hearts with Emily), even if you have no interest whatsoever in her being a romantic interest (even if you are already married), you get an event where Clint basically goes, "oh, I'm really happy for you two." Which is most likely just a byproduct of the game not mechanically differentiating platonic from non-platonic friendships until much later, but really makes Clint look like a possessive asshole in a way that probably wasn't intended.