I'm having a similar issue that I'm pretty sure I know what I did that caused it, but I don't understand WHY it is happening nor how to resolve it. I'm posting it in this thread as it sounds related to me.
I had a vocal track with multiple take lanes. When I recorded 2 subsequent vocalists, I unknowingly still had that track armed - so it added their takes to this track before I caught the error. I was about to Comp this first vocalists track - all the other tracks are comp'd - when I discovered the weird problems: when I try to delete their take lanes in the original vocalist track, a few have multiple layers in that one take lane. (There are clearly multiple voices of one vocalist in that take lane audibly, I have to mute the clip multiple times to gradually silence each voice.) Also, when I Solo or Mute one take lane, ALL the take lanes in that track Solo or Mute. Deleting one of the offending take lanes does not delete the take lane, but it DOES cause many or all the take lanes to rename to the same take lane name (this is not consistent), AND they re-arrange in order. There is also one take lane that is empty, but it graphically is several lanes wide, and when scrolling through take lanes for that track it will sometimes stay on top of the other lanes while they scroll "behind" it. This empty take lane will not delete.
I tried grouping and ungrouping lanes as Craig suggested, no change. I unmuted all the desired vocalist's clips and muted all of the added-in vocalists clips, and then selected Delete Muted Clips for the track, then Remove Empty Take Lanes - and that got rid of most but not all of the "offending" take lanes, including the empty take lane mentioned above. But I'm left with the same issues - can't get rid of a few undesired ones, and the behavior is so erratic I'm not comfortable comping and hoping I can get the output I want as I work through the project.
I have already comp'd the other 2 vocalist's tracks, removed unwanted clips and take lanes; is it possible those were grouped to the identical take lanes in this track, and now these are "floating"? I'm not sure what else to do than trash this track and get the vocalist to re-record.