When you flatten a comp it creates a new clip in a new take lane. It should mute all other take lanes and have the flattened comp soloed. Could it be that after flattening you have un-muted or un-soloed the comp take. That would leave you with over lapping clips with the same notes.

Thanks - I just tried this.  For sure, it's not me changing any solo or mute status.  I just went back a dozen or so saves and selected a drumset track, flattened comp, then activated piano roll edit on both the main track and then the new comp lane and duplicates are in both.
 
I did notice that the original had a duplicate HH in a single track with BD/HH.  When I flatten this comp, the BD has 2 and the HH has 3, so Flatten comp is adding a duplicate that shows in the piano roll edit.

I usually end up with dupe notes because of copy/paste blunders. Never occurred to me they'd have their own Take Lane and I never use SV. Might help me locate them in the future. Thanks!