Those sound like "hot spots", aka a pre-blister.
When you saddle up in those pants again, take note of where the seams lie in relation to the location of the hot spots, and start narrowing down the source.
Figure out the source, and then fix it.
If they persist, you can get moleskin to put over the affected area as protection. Moleskin is a stinker to remove, and you'll still have sticky residue from it. Baby powder or Gold Bond is great, and rubbing alcohol gets most of the stickum off before powdering up.