Can't give a definite solution, but I've had something similar with strange pops appearing on audio tracks that I'm certain did not happen during recording - ie they somehow happen afterwards, usually right on a barline/join between samples.
I just do either a tiny fade-out over a fraction of a second to nuke it, or redraw the waveform to get rid of the blob in it.
If it's not the same thing you have though I've got no idea sorry!