Whenever someone clones or breaks a block from Chisel and Bits, the game disconnects all players, gives them a Timed Out message, and then the server acts like everything is normal. The Aternos page and the multiplayer screen says that all of the players are still online. In the Log and the Console, it doesn't show any issues and doesn't log that any players disconnected. Restarting the server causes the same issue: players join, get timed out a couple seconds later, and the logs don't notice it happened.
This is the last thing that shows up on the log before the crash. It registers that people have joined, but not that anyone got kicked.