I don't spend much time recording or editing MIDI but I saw something new for me today.  I had recorded a MIDI bass line, and most of the recorded notes included multiple note events.  
 
Here's a piano roll pic:
 

 
And here is the event list:
 

 
I played each note only one time, but multiple note events were recorded.  I'm assuming this is just the aftertouch changes, but I hadn't seen this before.  Have I just not been paying attention?  The piano roll treats the multiple notes as a single note, and you can adjust where the velocity changes within a note by click/holding between the colors and sliding back and forth.  I didn't see anything about this in the help.

What input device did you choose in the following sections?
 
1. Edit > Preferences > MIDI > Device
2. MIDI track's Input field

One possible explanation is that your keyboard’s local control is set to on. The on setting can send double notes. Turn your local control to off. Does this solve your problem? If not then there is another problem.
 
There is a cal that will delete all of the duplicated notes. I believe it is called undub or something like that, I’m not at my music computer.
　
　

The cal to get rid of duplicate notes is called, undupe.

OK, I figured it out.  There were two takes, and the white/dimmed portions of the notes I'm seeing are actually notes on the muted take.