Alright, this is my first in-depth Theorycrafting, so bear with me.
Let's start by examining the immediate circumstances of the event.
Ciro mentions that she feels like she was "stabbed in the heart" but that she is "okay now". That's a few seconds from "bleeding internally and feeling mortally-wounded" to "as okay as ever, which may not be much but is still a lot better than before." This proves that it was no mere mortal wound.
One more thing: One theory which I nixed was the idea that it was just "exposure to the Arena". However, why would this affect Ciro, and only now?
Well, there's the fact that Ciro is the one whose Soul Charge stuff seems to build up the fastest, so maybe his/her soul would be most susceptible to shocks like that. If such things work like, say, water flowing through the sand, that would make Ciro the unlucky gully. However, this theory fails to explain such things as why the screens matter so much for this, what this "shock" is, and why having a fast-charging soul makes you more susceptible to it...and, above all, why it stopped.
Now let's go backwards, update by update, which is a lot more tedious than I would have thought.
Update -1 Summary:
Everyone prepares to fight Mega Man, who tells us to chill. We get some expositiony BS about how the multiverse is flexible and we were lucky enough to run into him. I don't think there's much to worry about here.
Update -2 Summary:
We fight the Mets, with Ciro really missing with the Clot Cutter. Ciro complains about how
Attack Attack Attack strategy sucks, when MM shows up to save us from the last Met. Again, none of this seems to relate to the bleeding...unless it had something to do with dropping the Clot Cutter?
Update -3 Summary:
We smack Mets around. Wow, this is kinda fruitless.
Update -4 Summary:
We scan ourself. Hm...Anyways, Al makes a double entendre which Rilitia completely misses, as he retrieves a sword. We teleport to the arena. Scanning Ciro seems like it might have something to do with it, but I can't imagine what. Those of you who want to investigate further, it's on page 190.
Update -5 Summary:
5 is one of those numbers which if I had a "do X in Y turns" would be obvious to do. Let's look at this turn carefully.
We spend all our money on Tips. Something tells me this didn't cause internal bleeding and psychic mortal wounds.
Update -6 Summary:
We head to the Market, Ciro talking about the merits of piggyback rides which are then forgotten. This is an unlikely candidate.
Update -7
I'm skipping the interlude for obvious reasons.
Ciro piggybacks on Rilitia, the Interlude begins.
Update -8
Al's soup is confiscated. Al and Ciro chat. Al points a sword at us, and Rilitia joins in, wondering why people can't move between dungeon levels freely. Al rejoins us and hugs Ciro. The Shipping Grid recalibrates. While this update has a lot of climatic stuff, and it would be amusing if affection for Al caused actual physical harm, there's no evidence that this is the case, no proposed mechanism for this to take place, and the timing is not suggestive of a timed effect.
Update -9
I'm not counting that explicitly non-update joke.
We run into Al, it seems. Rilitia mentions that she has no memory about what happened...before. Ciro says she's hungry. Al invites us over for dinner. Again, as above, it's an unlikely candidate.
Update -10
This is another one of those numbers where you would expect something if it was a delayed effect.
And what do you know, guess what we did?
We should check back earlier, compile arguments until we have a solid one. Basically, my guess as to what happened is:
1. We cheated the save system.
2. We got HP>MHP
3. This, possibly due to paradox but more likely due to "overflowing" with blood, caused stress inside Ciro's body.
4. This caused a timed effect to activate: 10 turns later, we would have a sort of internal bleeding thing.
I need to check this more thoroughly, but it makes sense to me. For future reference: This turn is on page 168.