I think the bug with this is not that one cannot trap souls with the suitable gems, but rather that the message itself is erroneous.

Repro:

I have a war axe I enchanted with soul trap and an empty black gem in inventory. I kill Commander Maro on the dock, get the message, check inventory and lo! the gem is filled.

If it takes more than one hit, the second may give the message because it can't apply it again?

Oh, interesting thought. That would imply someone is using an accumulator for a boolean. Not a good choice.