On a formal level, there are always a plethora of logical issues with gameplay and story because you start deconstructing the abstract shortcuts that all storytelling requires. You start deconstructing your own suspension of disbelief.
Games are often criticized when their gameplay doesn’t reinforce the themes of or characters in their story. This interplay between systems and stories is what fascinates me most about games, but even I have to admit that it’s a rather odd criticism when you think about it. I’m not really criticizing the story: not the narrative, the themes, or the presentation of such, nor the pacing, the dialogue, or character development. I’m also not really criticizing the gameplay: not the controls, the difficulty, the balancing, nor the entertainment value. Instead, I’m criticizing how all those things interact with each other. It’s not really a criticism of art or craft but of form, a meta quality that seeks to judge how well a video game is at being a video game (and which—unfortunately—can lead to distracting discussions about the definition of “video game”).
Here, at this formal level, when we start dissecting the meta elements of a game we risk descending into an endless spiral of cynical deconstruction. At this level, there are always a plethora of logical issues with gameplay and story because at this level you start deconstructing the abstract shortcuts that all storytelling requires. You start deconstructing your own suspension of disbelief, and no medium can survive that.