At two points in Captain America: Civil War there's some unconvincing CGI. One is a rubber character model falling like a ragdoll and the other is some iffy greenscreen during a key scene. And that's it. That is literally the biggest criticism I can muster about Marvel's magnum opus.
To call Cap 3 the best film in the Marvel Cinematic Universe is to sell it short. It is borderline perfect, a thrilling, character-driven blockbuster that stands above the rest of the superhero genre, from classics like Superman: The Movie through genre stalwarts like Spider-Man 2, and even out-thrills The Avengers; it is second (or rather fourth) only to Christopher Nolan's The Dark Knight Trilogy (and actually better if you view it from a purely comic book metric).