I had the same problem initially when the game came out, and it seemed to go away after some patches (was always intermittent), and then the other day (post patch 3.0) it was back.
I notice that when it occurs it is (for me) accompanied by the menu screen having the circles/hex overlay thing that normally only appears as a backdrop in non-VR mode. If that's there, then the target markers detatch in game also.
Currently it's working correctly - and the only thing I did was drop my Super Sampling from 60% to 50% so maybe try a different SS setting (though I'm sure I've run on that setting before without issue). Though that could also have been unrelated as I haven't tried setting back to 60% to try to replicate.
