One of the stupidest things done with holodeck safeties was in Voyager's Spirit Folk. In the episode, Tom Paris and Harry Kim are on the holodeck, messing around with an exposed computer terminal while the program is running. A mob of holographic villagers shows up, and one of them fires a rifle which damages the computer. After this, the computer warns that safeties have been disabled. Which means that while safeties were active, a holographic bullet somehow damaged actual components of the holodeck.
Some people over the years have attempted to explain this as the holodeck safeties just protect people from being injured, they don't prevent equipment from being damaged. Unfortunately, this means the device which is meant to protect holodeck users from harm in the simulation is itself capable of being damaged by the simulation, which is a very shocking oversight when you think about it.