Unfortunately, there are quite a few limitations when it comes to working with sequence clips inside Adobe Premiere:
Only clips that have associated project item can be manipulated. Text or Shape layers will be ignored.
If a video/audio/image layer is cut into multiple parts, then all of its instances will be affected.
"Display the project item name and label color for all instances" has to be enabled under Project Settings > General tab. (File > Project Settings > General...).
Unfortunately, there is no way to group multiple events into an undo group in Premiere. So, when changing Label colors for multiple items, Premiere adds each event for each item into the history.
One way to fight it is to increase History level to max allowed value 100. To do so, open the History panel (Window > History) and choose Settings from the Flyout (hamburger) menu.