This happens when editing MIDI in sessions created by older versions. When you select a portion of a MIDI clip on the timeline and delete it, MIDI data including notes remain on the track outside of any clip and continue to play back. Same if you separate the clip on the timeline and delete one of the two new clips. It can be almost impossible to select and delete some MIDI data from the timeline. If you do manage to delete the notes, consolidating the remaining (intended) clips on that track will cause new clips to appear where CC data had existed in the deleted clip. Opening the MIDI piano roll and adding a note causes the phantom notes to disappear.
Seems to afflict both Mac and Windows users. Personally, I experience it in PT 12.8.2 on Windows 7.