Piano Roll Gremlins

I'm not sure how I'm going to clearly describe this, but here goes.  I had to repeat this several times to ensure I'm not just exhausted after 3 15-hour days of working on this project.  Maybe I'm missing something really simple, but I'd really like to know if anyone else recognizes what's going on here.  I'm doing another MIDI mockup gig and am now experiencing the strangest issue with piano roll edit.  For instance, on a drumset track, if I grab a note and drag it up from say, BD to Snare, the note moves, but leaves the original note behind, as if there were 2 copies of each note on the track.  I have no idea how I would have created a duplicate of the individual part if I did, and I couldn't tell that there was more than one copy until I grabbed a single note and moved it.  However, the strangest issue is that if I click the leftover note with the mouse (with the move function), I can hear the note play as normal, but it doesn't sound during playback.
 
Does sound-on-sound have anything to do with the multiple layers?  If it does, it would be nice to select everything except the bottom 'layer' with the box select tool and hit delete.  This seems to be consistent in another track where I found what appears to be 4 copies of the recorded performance.  If I individually delete the top 3 notes, the 4th still shows on screen, but doesn't sound during playback.  
 
The only thing I could add that may be helpful, is that I believe this is only happening on tracks that I have used 'Flatten Comp' on to cleanup the workspace.
 
Tell me I'm just tired and missing something so simple...   :/

Right.  I do have duplicate notes.  The problem is, if I move or delete the top duplicate, the bottom still shows in piano roll, but does not play back.  In a large edit, this is beyond confusing.  

I'll assume I had a mittens moment with the duplicates.  But yeah, still baffled with the remaining note not sounding during playback.  If I grab the note and move it, I can hear sound both when grabbing the note and every pitch as I drag it up or down the keyboard.
 
I'll look into that CAL script.  Might be useful in my case.  Gotta get the gig done, going ahead with individually erasing & checking notes o.o.

CdrDave
If I look at the clip in track view, I can see that the MIDI notes I deleted are no longer showing on the clip itself.  However, they are very much showing in piano rollout view.   

You might have a different midi track in focus in the PRV.

Ok, so after a break, I was able to re-trace my steps for actually getting this to work.  Only dragging this out to try to understand exactly what happened.
 
So, the track clip had a lock icon.  If I uncheck Clip Lock>Lock Data, the blue lock goes away and I get the issues mentioned above.  I assumed I need to unlock it to edit it (not even sure why it was locked - a function of collapsing lanes?).
 
However, if I leave it locked, go into piano roll and select all, delete, it gets rid of the duplicates, leaves the original and now plays back....on the track with only 1 duplicate.
 
I was able to repeat what caused the doubling.  On a separate perc track, I used "Flatten Comp" to combine the 3-4 lanes into one track for less clutter and easier editing later if needed.  I opened that clip in piano roll and now have doubled notes.  Flatten Comp is definitely creating doubled notes in the entire clip.  If I lock data, select all, press delete, it will delete the duplicates and leave the original line working.
 
Is this working as intended?  If so, why?

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.

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!