The usual cause of this is lost steps on the upstroke. The z axis tries to retract to its safe height, but something happens - it can be a lubrication failure, a gall in the slides or screws, something out of parallel, too heavy a spindle assembly, too ambitious an acceleration setting - and it doesn't get to the mark. In an open-loop stepper system, it will assume it did get there, and count the correct number of steps going down, which takes it lower than it's supposed to go.
Other causes can be the tool pulling out of the collet - spiral flutes can catch and pull - or a set screw failure at the coupling.