What immediately bugs you when watching an episode? Mine is when they transport someone sitting down and they reintegrate in a standing position (or vice versa). Sure, the tech is near magical but my suspension of disbelief pretty much snaps when they do this.
Just once in a Star Trek episode, I’d like to see the antagonist try to seduce a crew member and be told “you’re not my type.” The ENT episode “Rajiin” was especially ridiculous in this area.