Shock Ability

Well, characters don't seem to have any MP if they don't have the magic command, UNLESS they learn a spell via an item. So for example, if you equip imp gear and they learn imp, they will now have a MP meter even though they have no magic command.  It's kind of a bug, but it works that way. 

It's not a bug in terms of the original game. It's precisely intended to work that way, as blanking out MP is a way to hide the fact that any of your main characters could learn magic under the right circumstances.

In addition, temporary guest party members like Leo are unable to learn magic due to their actor ID being beyond the bounds for learnable characters. If you didn't change his ID in your hack so you could enforce his "no magic" status, that would also cause a problem with MP-battle related things.

Both can be worked around, but if you're talking about a hack that is closer to the original game in this regard, it will be more difficult.