this is an issue i observe in c6 but just encountered on a nuendo 4 system as well, so does not seem to be version-specific.
the issue on top of this issue is reproducibility at the moment; what happens is, i may have a locked markers track in a all-audio project, and while chopping away audio, a stray marker on the [locked] marker track will just move to the place in the arrange where i have just performed an audio editing operation (usually i will execute a number of different macro’s in succession so i have not been able to tell yet how to trigger this behaviour. most often though, this will happen when doing ‘cut time’ or ‘delete time’, and switching between the range and select tools).