I think there is only one of those bugged anomalies left and it's on Elvren IV. Near the last device there is an anomaly which can be seen, butt it's just around 90% above ground, 10% is stuck in the ground, so you cannot scan it. I saw this bug today with my science toon Jhamel.
More information is always great. I'll see if we can send an away team out there to take a look as you described.
If you have an extra Away Team handy, any Klingon Planets I have landed on say there are 4 to 6 Anomalies, and I have only Ever Gotten 2, if that, and the Scan on Planets for Klingons always points back to the Last one done, or Closest. Even then, it will not point out any of the next 2 to 4 that should be remaining.
(Come to think of it, that problem would probably occupy a couple of away teams)