If you found the Hunter Pirate, then yeah, it's the most likely cause (I think there might one other pirate that also brings innocents with them? It's been a while since I've hunted pirates). The only other thing I can think of is if you created a specialist with a Mediator, but you kinda need to go out of your way for that (and IIRC it also comes with a notification, so you'd know about it), so it's quite unlikely that that's the cause. There are also lovers that randomly spawn unsubdued in this game, but not in an item you just ventured into.

The Dancing Pirates can also have unsubdued Innocents on their boat.