I think I figured out what the problem is since the same thing just happened to me. Luckily I was able to figure out the problem.
When you have multiple take lanes but you don't have one selected via the comping tool as the "active" take, the piano roll will show all of the notes for all of the takes. Since you had copied a track it was two sets of the same data in this case.
Try this:
1) Open the clip in the piano roll like you did before and notice the two takes
2) Now go and select one of the takes as the active take with the comping tool. Piano roll should now correctly display just the info for one take.
3) Once you've selected an active take, the only way to get it to display the bad behavior is if you hold control and select more than one take as the "active take" with the comping tool.