I originally mentioned these two issues on the gift.physik.tu-berlin.de game server board, and prissi asked me to file a bug report. I tested them using r4136, but problems date back to at least the 102.2.2 stable.
The first issue occurs when one player builds a tram track under another player's (or the public player's) bus stop. The tram track cannot be removed, even using the remove track tool, but electrification can be removed.
The second issue is with bridges with removable pillars (In pak 64 the modern road bridge, high speed rail bridge, and the brick-stone viaduct have these). If a player builds a way under a bridge owned by another player, that way cannot be removed unless the player owning the bridge removes the pillars. Again, using the remove track tool does not help, just an error message "Ways not connected"
Fifty
Should be partially solved in rev 4151. The way-remover tool should work, the all-purpose-remover needs to be fixed.