When material is in the song track, one can mute it so it doesn’t play in “follow host” mode. However, it still affects what is going on in the DAW. In particular, it affects the sustain pedal. It will un-sustain it so to speak. Therefore, muting those clips only turns off the volume, it does not turn off CC stuff like sustain.
The solution I assume is uncheck “follow host”. Easy fix, but it just deserves mentioning how the “mute” feature works so that people don’t go crazy trying to figure out why notes suddenly cut off. I tend to leave passages in the song track as a way to store them, in no particular sequence. I forget they are there, until I realize that the sustain is acting funky then I realize it’s because there is muted material in the song track.