Godzilla
It would have been a good idea to barricade Godzilla so it couldn't escape. For some reason, no one thought of that. So, the authorities have the arena with the baby Godzilla eggs inside surrounded, but Godzilla totally disappears. It kind of defeats the purpose, right?
Thor
At the end of Thor, the Bifrost is totally destroyed. There's no way to get out of Asgard, which makes Thor upset because then he can't get back to Jane. In the film after, he rejoins The Avengers gang like it's no big deal. If the entire point of the ending was to showcase how Thor was trapped on Asgard, why is he magically back with them?