That's weird. Has never happened when I did modifications like that.
Try disallowing another unit for a civ, for example, knight, just to see what happens... if you get no error, then something is definetly strange with the pueri.
Perhaps it has something to do with Pueri being a replacement unit. How did you set that up? Is it set as a replacement for horse archer, or is it a seperate unit, with horse archer being disallowed for civs that have it. Or are you treating it as a UU. For the whole Cog/etc. the units, I believe, are not set up as UUs but simply disallowed. Maybe you need to have an entry disallowing horse archer at the same time you allow Peuri. This all depends how you've set up the unit.
I don't know how UUs work or how to create one, but I suspect that the units shouldn't be set up as UUs but as ordinary units, then disallowed and allowed in the civinfos file. If they are UUs, then disallowing horse archer while allowing a UU, Pueri, may screw things up.
However, I'm just guessing.