Looks like it's the "GnomoriaModUI" itself. Started it without using any mods (deactivated them all) started a New game (standard settings, didn't change anything) and then played for nearly 1 day. Marked some trees for felling, some bushes for foraging, created two small farms and one pasture and build into the mountain nearby. I created a new squad and added one to that squad then.
When it became darker, the miners where nearly finished, so I dug a stair down. Then, one level below, i created two 7x7 rooms side by side (without any wall in between). When i tried to place another stair down in the middle of the other room, the bug already started. The command wasn't executed. I couldn't change the level of depth (thats when i realized that the bug has happened), and after around 5-10 seconds everything worked again, but the mouse was, of course, displaced to the rest.
I'm using the Steam version of Gnomoria on a PC with Windows XP 32-bit SP3.
Maybe it's because the GnomoriaModUI doesnt work with the Steam version correctly?
It already circumvents the whole "Steam has to start before the game can run" thing, so i can play Gnomoria with it without starting steam. But that bug happens after some time -.-
As I said, I didn't even get to day 2 and I only used the normal speed.