It might possibly be caused by silver left behind by the fixer, though it does look very much like a 'solarisation' effect. Any remaining silver emulsion would lighten the shadows (ie. areas which 'should' be clear on the neg) of the reversed negative image rather than darken it - it depends on what the scanning software tried to do with the image. Is there any unexpected colour to the film? Anything in the direction of the beige emulsion colour suggests a fixer problem.
Check the fixer by putting a drop on a piece of scrap film (ideally Pan F, if that's where the strange results are found), wait a few minutes until it is almost clear underneath the drop of fixer, then dunk the whole thing in a beaker with an inch of the fixer and agitate at normal intervals. Note how long it takes for the clear dot to become indistinguishable from the rest of the film offcut (this is how you are able to categorically decide that the film is cleared), then double that to give your required total fixing time.
If you find that this experimental time is more than the time you gave the roll when you processed it, then re-fix the negs. This can be done in daylight of course. Loading at least one of the strips on to a dry reel should not be too tricky, and will allow easier fixing and washing than having short pieces of film in a tray.