I think all the time travel confusion comes from the ancient one, that exchange with Bruce is what messes up everything. Her saying that there is a single timeline unless the stones are removed is what creates all the holes.
Instead they should have established that every time you time travel you create alternate timelines period and there is no way to get rid of them or fix them. That would have deaded the whole idea of trying to put the stones back in the exact spot, which is crazy, and basically created a bunch of realities where Thanos can't snap.
Then you can attribute all the inconsistencies to alternate timelines