If you bounce to clips - this should merge and note and controller data from different clips. There are a few CAL routines that remove duplicate data in the event you have exact note conditions at the same time stamp. You can also look at the " event viewer " to see if you have duplicate notes at the same time stamp.
I think in the Piano roll -you would have to grab the note and pull it up or down to see for sure - hold shift while you do it to keep the time locked, it would be a good visual tool if over lapped or covered notes would light up a different way. Maybe a bright red splash color.
RBH's post in In piano roll view is it possible to see notes behind notes in same track? was marked as the answer