I also have this problem when using my MPC1000 to send MIDI clock.
The Monomachine sometimes has hanging notes or will start to play on its own after I have stopped the MPC. I usually just hit stop on the Monomachine after I have stopped the MPC just to be safe. That works. But sometimes when trigger external midi tracks the hanging notes can create random weird patterns, have the recorder handy. To be honest for that reason I kind of enjoy this quirk. But other times it is annoying.