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- Compared to many other works in the Touken Ranbu series, where it is clearly established that tampering with history will have negative consequences and thus the characters should avoid it, Musical Touken Ranbu is fairly inconsistent in terms of what will change history, despite mostly employing the same logic, at least at first.
- In more than one musical, the Touken Danshi have to play the roles of prematurely deceased history figures due to Historical Retrograde Army intervention to ensure that history flows as intended, but you'd think the characters taking on those roles would go down in history because, realistically, the appearances of the Touken Danshi would be recorded in the books. Paraiso is particularly bad about this because it has two Touken Danshi impersonate a historical figure but then assumes that word-of-mouth would not have spread that there are two rebel leaders with the same name running around, especially with the Shogunate actively collecting intel on the Shimabara faction.
- Like in most Touken Ranbu works, there's also the nagging question of why, with their peculiarly colored hair and eyes and flashy outfits, none of the human characters notice that the Touken Danshi look out of place. Are the appearances of the Touken Danshi only unique to the audience? You could argue that in the beginning, but even the Historical Revisionists changed their appearances to be more human to blend in with Hijikata's faction in Musubi.
- Kousui reveals that the Government of Time will isolate the timeline from the rest of history and create an abandoned world if history is altered dramatically in any way. If one period of history abruptly disappears, what does that mean for the rest of it? Billions of people from the future would undoubtedly cease to disappear, right? How can there even be a future with one period in history missing?
- What is the purpose of the Touken Danshi in protecting history if the Time Government can simply isolate altered timelines from history and presumably replace them with the correct timeline?
- Tokyo Kokoro Oboe reveals that Mikazuki has established himself as a constant throughout numerous historical periods in order to correct timelines, but he has managed to avoid being mentioned in history books. This is questionable because, while Mikazuki only appears to recruit people who trust him or threatens them into working for him, you'd think that after several hundred years, some people would notice a pattern of a strange man appearing throughout history, especially since he influences significant historical figures, and record it.
- Are the Idol Singer segments canonical? The tone is so disjointed from the main stories that it would be easy to dismiss them as being noncanon, but the first plays provide an In-Universe justification for why they occur, implying that the Touken Danshi do, in fact, perform for an audience of Saniwa. However, what really calls into question the canonicity of these performances is how the Historical Figures also return to the stage to perform, either singing songs during intermissions when the Touken a Danshi leave to rest and change, or as backup dancers near the end of the play. The fact that even Historical Figures who died during the main story also return to the stage makes it all the more confusing and jarring, but the Touken Danshi, nor the story, acknowledges them or explains why this happens.
