I don't know if it's user error and is expected, but sometimes when I try to use the right mouse click to mute a track, the top most folder gets muted as well which is quite annoying. I have been able to reproduce it consistently on a brand new project. 

Steps to reproduce:

1. Create a brand new project with 3 audio tracks
2. Create a new folder and put 2/3 tracks in that folder. Move the folder to the top of track view. 
3. On the third track(which does not belong to the folder ), enable 2 take lanes in the track 
4. Populate all tracks and take lanes with audio.
5. Now right click on the audio from the take lane to mute it. You will probably see that the first folder gets selected also. 

You may ask why not use the mute feature from take lane, it's because I'm importing some projects from X1 and some take lanes have more than one clips in them. I just wish to mute couple of clips only from that take lane and not the entire take lane. 

I have this problem as well. Only just worked out what it was. Very annoying. When you right-click to bounce two midi clips, it selects everything in the first track folder and then bounces it all!!! I've lost a few hours to this bug.

I have a few workarounds to share
1) Having selected your clips in the take lanes that you wish to bounce, don't right-click in the take lane, instead right click in the main track's lane.
> 2) Use the Track and Clips menus on the top left of the tracks windows.
3) Bind a shortcut key to Bounce to clips and use it instead.

 Yes! This is the same problem I reported separately as V-Vocal selecting multiple tracks. Maybe the work-around is to keep them in separate folders.