Last week I processed a roll of Pan F 120 which is pretty much unusable due to being covered in small black spots. Below is a detail of a neg scan of one frame - there are hundreds of these dots, more in the denser areas. The pattern seen here is present in every frame of the roll.
The film is in-date - it was bought earlier this year from B&H and expiry is Jan 2013. It was exposed in a Zero Image pinhole camera. Processed in Adonal 1:50 (Rodinal) followed by an acid stop and Kodak Fix then Hypo Clear. I suspect the problem is a combination of the film, Adonal and acid stop. Some searching suggests that Pan F is a somewhat fragile film. Funnily enough I hadn't used acid stop for years - always used water until recently on a whim I decided to use acid stop. I have read that the Rodinal solution is very alkaline and the sudden change to acid can shock some films. Would that cause black spots, which must be some sort of silver clumping? What the hell are these black spots anyway?
I still have a couple of rolls of the Pan F left and will test with Adonal and water stop. For now I've switched to Tmax 100 for the pinhole; not keen on fragile films. Below is the full frame positive where the black spots show as white flecks.
I don't believe the spots are the fault of the film. I suspect your water source first, or undissolved chemicals. The spots appear to be tiny flakes of some sort too often found in unfiltered water.I don't think the acid stop bath caused the problem, but there is no need to use it except to stop development more quickly. I have used plain water stop bath for years with no problems.
You might try using distilled water for your final rinse.