Actually, how it works is that the core building (governor's palace) has a -1 bonus to siege weapons. A unit with a negative weapon bonus becomes impossible to recruit, and enables to us an easy way to create reforms. It's basically one such reform per faction we can do this with (as all "siege" units are "upgraded" at the same time). The Romani reforms for instance use other, more "expensive" technical means as they have more than one reform.

I see now that there is an unfortunate side effect to this, we didn't think of mercenaries being able to "upgrade" to a -1 weapon. Apparently the game engine thinks that means +3 for retraining purposes. We could fix it by duplicating the unit and having the mercenary kind use "heavy" weapon rather than siege, and we probably would if EB1 wasn't considered finished. Also, it's really easy to not exploit the bug, so I don't think we'll spend any effort on it.

Still, thanks for reporting! I never knew about this bug before.