I noticed that this is the only mission that this happens in and it also doesn't happen in multiplayer. I tried to reload by dragging a new magazine onto my gun in the inventory, but the magazines that I was dragging were disappearing too. I also tried dropping and picking up my weapon again and switching weapons, and nothing changes. I also tried to pick new magazines off of a dead body, but every time I right-clicked on a new magazine or dragged it to my person, it vanished from the game completely.