I've only seen it happen one time so far on the bottom active rune (in the case it was a regeneration rune). I ran through river over the spot where the rune spawns and nothing was there, we had no wards around the area. And when looking at the minimap it displayed that a regeneration rune was there, spawned and available. I was unable to ping it out on the ground or on minimap. So visual bug. From what I recall it only was visible when it was in vision. So when I walked away from it and the area was fogged, it no longer showed, but I walked back in to see and it showed on the minimap again. Upon looking at the replay of: 3751242232 at 23:20. Pudge hooks it backwards twice.

Repro Steps:
Have pudge hook and active rune out of vision away from the original rune position.
Take an enemy hero and walk over the rune spot.
Look at the minimap, it will display the rune as if it is there, but it will not, nor will you be able to ping this on the minimap

The active rune shows on the minimap as if it exists, it does, but it is moved out of position due to pudge's hook.

Expected Result:
This is intended. OR
The minimap should not display the rune on minimap when it is not there (just moved) AND/OR it should update the location of said rune on minimap when it is in vision of the enemy