Creating a video game story is hard. Not only are developers given the gargantuan task of coming up with a compelling narrative that needs to last potentially tens of hours, but they also have to make sure that it complements and supports the ideas found in gameplay, too.
Because when these elements don't mesh, you get strange inconsistencies. For instance, almost all zombie games rely on the idea that when people are bitten in cutscenes they become infected, but this becomes a plot hole when the player can take bite after bite during gameplay without it ever being a problem.
Some plot holes are more pressing than inconsistencies between a title's story and gameplay however, and even the most critically acclaimed narratives in games have gaping holes and/or leaps in logic that fans have been discussing for years. Even though developers would like players to get over them, fans continue to attempt to fill in the gaps and explain away the story problems of their favourite games.
Still, with no official explanation ever coming, players are starting to accept that these often-discussed plot holes may never be solved.