To reproduce my problem:
Start up laptop (Macbook Pro, version 10.8.5) with it connected to an external monitor (Apple Thunderbolt Display) that has the mouse and keyboard connected to the USB ports on the external monitor. (At this point, USB mouse and keyboard still work fine)
Remove thunderbolt display cable from laptop.
Reconnect thunderbolt display cable, re-enabling external display. The USB mouse and keyboard do not work and are unresponsive.
Interestingly, the ethernet connected to the external monitor does work, which makes me think the issue is isolated to the USB ports. Connecting and reconnecting the USB devices to the external monitor doesn't work either.
The only way to fix the issue is to restart my computer.
Any ideas on what's going on and how to fix it?