1) I think you can fix a "phantom" command in device mode by simply editing the device button mapping. Just rename a label, click done, update the remote.

2) The activity commands are re-grouped by device priority. On the 6xx series, the device in the left column has top priority. The next device (in the next column from left to right) has 2nd priority and so on. On the 880, you will have to figure this out yourself.
Workaround 1: If you need a command from a lower priority device to be grouped with the ones from a top priority device, simply add a "bogus" (a do nothing) command in the top priority column along the same row (line), or
Workaround 2: Teach the command to the top priority device.