Okay so like the time travel is a little funny but it doesn't create paradoxes and the movie follows it's own logic up until literally the very last scene. But there's two big problems with it that bother me.
So here's a summary of the time travel in Endgame based solely on the description given by The Ancient One and Professor Hulk, but I'm explaining it more thoroughly. The movie does not actually follow this logic completely but I'm taking this description to be more accurate than the events that actually happen:
So if you go back in time, it creates a parallel universe that poofs out of existence when you come back which is why they can't do any harm and don't have to worry about running into themselves or anything. If they grab something and then come back, while the rest of the universe disappears, as long as that object came through the quantum realm with them, it doesn't disappear. The only exception to this rule is the infinity stones. Removing any one of them will cause the parallel dimension not to disappear. And then if they try and go back in time again, they quite specifically go back to that same parallel dimension they've created until all the infinity stones are returned.
So here's the first thing that's bothering me. They remove Gemora from the parallel dimension and then Cap takes back all the infinity stones, causing that dimension to disappear. When they removed the infinity stones, the dimension never went away and Cap must have gone back to the same dimension when he went back the second time. Now that dimension should be gone. So if they go back in time again, and enter at a point that is after they removed Gemora, will she be missing or will this count as a new dimension kind of like all the enemies respawning and all the items resetting in a game? Could they theoretically have more than one Gemora if they did this multiple times?
And then the final point here that really bugs me is that if this is possible, doesn't it actually solve Thanos' problem? They'd be able to get infinite resources from "back in time" but every time they go back to their own dimension, all of the things they took would reset.
The other problem I have is the one time the movie breaks it's own time travel logic. It's when Cap returns as an old man. He totally could have gone back to live out his life with Peggy and grow old and then return through the quantum realm. But what happened instead is that he lived out his life to the time he had traveled back from and actually met everybody there. There's two explanations for this.
1: When he traveled back in time, he went to the same dimension as the one he had started from and then lived his life up until the point he came from. This is how time travel works in most movies such as Back to the Future. The movie specifically states through dialogue that this is not how time travel works.
So lets's assume it's the second option then.
2: Cap actually stayed in the second dimension. The second dimension should have it's own Avengers and Thanos and everything so the final scene may be from within that 2nd dimension. This creates a whole host of problems, though. The dimension created by time-traveling is supposed to poof out of existence when the time-travelers leave. So if Cap never leaves, the other dimension actually stays. And then this should create a looping effect. If this scene actually is within dimension 2, then we just saw 2nd dimension Cap leave for dimension 3. This will continue forever. The only way this could be stopped is if, in fact, dimension 2 poofs out of existence when Cap dies. (I don't think this is the case and I'll get to why later.) If that scene really does take place in dimension 2, however, dimension 1 Avengers will never get to see Cap again and his shield will never be passed to Falcon. Also, only people left behind in dimension 2 will keep it existing, not objects. If Tony accidentally left any item of his in dimension 2 when they tried to get the infinity stones the first time, the dimension would never disappear even when the infinity stones were returned. And that even calls into question what counts as an item from dimension 1. Is the air in Tony's lungs not from dimension 1? I think if leaving something behind would cause the dimension not to disappear, then breathing would also cause it not to disappear. So clearly objects left behind don't matter. I know they're planning a "Falcon and the Winter Soldier" show which, given this logic, must take place in dimension 2 since Cap never returns to dimension 1. I assume Cap is going to die of old age soon, so in order for this show to exist, it must mean that the only thing that can keep dimension 2 open is a time-traveler from dimension 1, even if they're dead. Dead time travelers don't count as objects left behind.
So, to end that little rant, the thing that bothers me is that there is, in fact, an explanation for the final scene with Cap, but it's a terrible explanation (see "Dead time travelers don't count as objects left behind").