This is a common issue users encounter in Cubase. To solve this, go to Studio Setup > MIDI Port Setup, and deselect (uncheck) the boxes that correspond to your control surface under In 'All MIDI Inputs'. Or you can simply change your input selection for each MIDI track. Under track Inspector, change your MIDI input selection from 'All' to a device that's not your control surface, or 'None' if you don't want them to accept any MIDI input. Alternatively, you could also edit the Cubase Preferences and deselect the 'Record enable selected track' box.