Probably not, but at least one thing to check out for when it rears its ugly head next time. I noticed my drum pad double triggered a note when looking in the Key Editor. I removed the extra MIDI note, a very weak and hard to spot one, and tried to merge the tempo again … et voila! It worked. I don’t think I’ve ever thought of that solution so it was pure luck. Hard to complain. So … check for that next time it happens! 
It’s a great command but it seems kind of fragile? Any other things that can go wrong you’ve spotted and care to share?
Oh, time base should be set to linear for both the tapped track and the actual music before invoking the command.