Here's a question that isn't answered in the rules as far as I know: When is a mutiny over?
One ending should be when the CO is dead, but then we usually have fighting spilling into multiple rooms, with marines, mps, and CIC staff fighting for their lives. When the CO dies, there's no announcement like the xenos receive upon the Queen's death. So inevitably, we have Mps and marines killing each-other until one side is dead, or the participants are in a position to take stock of the situation.
What about if the mutineers lose? Is it just the first group that is considered the core? What if more marines join in? There's no way to track any of it.
This raises a second question: Why do we always have to resort to lethal force? Mps are given non-lethal options, several of which have no real time besides a mutiny where using them would be appropriate. Instead, MPs take the beanbags out of their tac-shottys, and fill them with lethal rounds. What else can we expect though? Marines simply don't have access to non-lethal force, and when it is used before lethals, it's usually right up until a taser or gas grenade goes off. And why does lethal force always end up being as-lethal-as-possible? Targeting someone's head is shitty and it could be argued that deliberately doing it is breaking the rules, you know what you are doing*.
There's dozens of other issues and inconsistencies. If the XO wasn't part of the mutiny, but for some reason didn't die or otherwise participate in the defense of the CO, is that XO now in command? Is the original A-helper in command? Is the highest ranking, surviving officer in command?
Much of this rarely makes a difference, usually because a mutiny results in or is catalyzed by the marines losing the fight on the planet.
This is also a problem. There's no antags. MPs are kind of designed to be a stopgap for low-level shittery to prevent staff from being overwhelmed with ahelps. But because MPs are IC, they can't acknowledge this fact, they have access to almost no investigative tools, they are random players with no necessary incentive to actually perform their job right. They are essentially security from regular SS13 stations, but they have 0% chance of actually arresting a danger to the ship in non-event rounds. The only time they are useful is mutinies, where they really just amplify the amount of damage to the ship/crew.
*Damage bleedover happens. Also forgetting to retarget the torso after doing medical work on someone can cause decaps.