10 Most Nonsensical Plot Holes In The MCU
1. Loki Should Have Been Erased When Cap Returned The Stones
In Avengers: Endgame, when 2014's Thanos, his Black Order and his entire army travel to 2023 but don't make it back again, that means that their original timeline would have been one without a Thanos. Avengers: Endgame tries to resolve that issue by claiming that Captain America returning the Infinity Stones stolen in the Time Heist closes off the branching timelines caused by their removal, thereby nullifying any changes made. The Thanos & co. that were disintegrated in 2023 were therefore orphans of a now-nonexistent timeline: spilled milk that Tony Stark's sacrificial 'snap' then mops up.
The same rationale prevents there from being a 2012 where Hydra have been tipped off that Captain America is on to them, two years before they were due to show their hand - or where 2012's Cap has been tipped off two years early that Bucky is still alive. 2023's Cap returns the Time Stone at the moment it was stolen, closing down that branching timeline as the Ancient One requested.
The presumption is that, according to the tortured logic of Endgame and Loki's time travel mechanics, that's why the Time Variance Authority didn't come down on the Avengers like the wrath of Kang: because Cap pruned the errant timelines and Stark effectively pruned the variant Thanos et al.
However, if that was the case , Cap returning the Time Stone should also have removed any need to prune Loki himself. After all, 2012's Loki didn't travel in time when he absconded with the Tesseract, he just hopped a few thousand miles into the desert. He was still in the branching timeline caused by the removal of the Time Stone, so Cap returning it should have erased him, too.