The kde default explorer dolphin does.
It creates them at the root of separate partitions (or maybe only network mounts).
Basically as a fallback to moving it slowly into a local trash.

You probably have the system mounted elsewhere and are accessing it remotely with dolphin would be my guess.

Last time I encountered it I found no good solution, it's very anyoing.
Best workaround is to create a file of the same name as the folder, that way at least it stays empty.