I was happy to see that I’m not the only one who fights with this. I have a few theories of my own, as I see this sometimes when developing my pinhole camera paper negatives:
I typically only see this if my paper is overexposed. If properly or underexposed, I don’t believe that getting the paper in the developer unevenly should matter much as long as its fully submerged within a few seconds.
Another thought is to make sure that you have enough developer in the tray – at least an inch? Anything less, and the paper is likely to surface in places and develop unevenly. Agitation helps; I lift and lower the tray in a rhythmic fashion to generate some gentle wave action.
I’m no expert and haven’t been doing this long. These are just my own observations.