This is not isolated to Beatstep, I'm having the same issue with my MIDI set up using RM1X as a sequencer. I'm running 1.0.3.2. It totally locks up and won't play via midi in or the keyboard. Like pants and Oeconomo say, I can clear by powering off and on, or toggling the sequencer play switch.
It seem to be occurring if the Microbrute is sent 2 MIDI notes at once, but moreover, if it is sent notes in rapid succession, possibly because the notes are overlapping in time. I will test to verify overlapping notes and update here. Regardless, I just got the Microbrute and was liking it. Will have to get rid of it if it's really this crippled in a MIDI set up and it cannot be fixed with firmware update.