Spoiler
My big problem from a logic point of view - although I'm generally not much of a stickler for plot holes - is Captain America's ending. It sent the film off on a surprisingly wistful note which I liked and it "worked" in my opinion, but it totally contradicts the time travel logic they establish in the earlier scene where they rule out killing Baby Thanos. If killing Baby Thanos in the past doesn't eliminate Thanos and his influence from the rest of their present timeline because that past is simply "a new future" for the person who travelled to it, I don't see how he can travel back to the past and then progress forward through time back into his own past (the present). This would bug me far less than it does if they'd not spent so much time trying to establish an alternative schema for time travel (explicitly in opposition to eg Back to the Future) throughout the film.