I don't know, but I would do some searches on common JM diseases (verticillium wilt, etc.) and see if you can figure it out. Some diseases can be treated with an anti-fungal spray or mix.

Good luck!

That stub is your problem. It probably should be removed, although it's a little late.
Mike

Mike, what do you think? I'd remove that stub (look up proper pruning cut before doing so) and then have an urge to spray with something....maybe an anti fungal, I dunno. regardless I would clean my pruning sheers afterwards.

It looks like the stub is dying and nothing else. I'd still saw it off so the encapsulation process can start as soon as possible this spring. As it is, it's going to take a awhile and look bad the whole time. The broken branch should have been cut where the branch originated rather than leaving a stub.
When pruning Japanese Maples, the branching pattern should be of the utmost consideration so you aren't left with a dying stub and congested branches.
Mike

Thanks everyone....I took the pictures to the local nursery and was shown where to cut and told not to spray anything on the cut, just let it heal naturally. Yes I definitely now know my mistake. I cut it off yesterday and the inside wood looked pretty clear and clean, but I guess I won't know for sure if it is going to make a full recovery for a while.

Thanks again for the help!