It has been almost three years since the movie first released so it had me thinking. I remember when the film first came out a lot of people were not used to seeing a superhero film that was this complex and thus turned every single thing that wasn't spoonfed to them into a "plot hole" and held it against the film.

Then overtime people stepped up and explained most, if not all, and put these issues to rest. I was curious if people still had things that they never understood/didn't make sense that they would like to post in a civil manner so we can clear this up once and for all in one simple thread without going off topic.
Having seen and told about every single plot hole that exists which I easily solved I was wondering if there were still some leftover that people would like to understand properly.

Please post them here so we can get past any remaining ones.