I did have one batch of primers (Winchester SP) where the anvil was set too high. No problem with them dropping through the pickup tubes, or the primer magazine, but as the primer slide moved them out, they would get hung up in primer magazine socket. Sometimes it would tear the anvil off, sometimes it would deform the primer, but I would always have to dismantle the primer system and remove the shell plate to clean up the problem. As soon as I switched over to another batch of primers, the problem went away.
If primers are getting hung up in the primer magzine, clean it up as described above, and check for damage. Also, check the bottom of the primer magazine for burrs around the hole. Sometimes they get dropped and it peens over a little bit of brass. Use a tapered reamer or a round file to make sure there isn't any brass getting in the way of primer movement.
As mentioned above, if you need a new magazine, I have them.