Along with the other suggestions could it be something on your fingers? Are you using tongs or handling the paper from one tray to another and then touching a new sheet?
http://www.jeffreyglasser.com/
I was going to make a similar suggestion.
If you are handling fresh paper with hands that have been in developer or fixer, you could be putting invisible spots on your prints that don't show up until they are developed. The same goes for tongs and utensils.
I learned the hard way...
So, now what I do is use chopsticks. Put the ends in a pencil sharpener and sharpen them just enough to round the tips off. Not enough to put a point on them. Get a dozen of them. You can usually buy them at the grocery store.
Keep them in a beaker full of water. Instead of resting them on the side of your developing tray, return them to the beaker and rinse them off between uses. It takes a little bit of practice to be able to "chopstick" your prints but, once you learn, you'll always have a clean, fresh supply of utensils to handle prints without getting your fingers wet.
You can get blue Nitrile gloves at Lowes/Home depot for less than $10.00 per box of 100. They're cheap enough that you can change them a couple of times per session.
Finally, I have developed the habit of handling wet paper with only one hand. I manipulate the prints in the chemistry with my right hand, using the chopsticks. I keep my left hand in my back pocket. Then, when I handle dry, unexposed paper, I only use my left hand, keeping my right hand in my back pocket.
That's a habit I developed when working on live electrical circuits like TVs, etc., to keep from getting accidentally shocked. Then I transferred that habit to the darkroom when I started noticing spots on my prints.
I agree with the others. Post some example pictures so we can tell what's going on.