Bob,
I have gotten to the point that I put all my cases in 50 case trays so I can look the headstamp over carefully before I clean the cases. I have had .380 cases screw up things on my 9mm press and .44 are about the same when you are doing .45LC. Same deal with .40S&W and any of the automatic cases about the same size. There may be a better way but I haven't found it (yet).
For a while when I was getting set up on 9mm, I deprimed and sized on a single stage (before wet cleaning) and that is when I decided having the primer pocket up would solve the problem. It's another step but the case feeder makes up for having to handle them an extra time. That also helped find the Berdan primed 9mm. Now I just use the universal deprimer and clean before loading.
Another thought, have you had a .357 get in with your .38's?
I have found quite a few .38 rimless in with my 38's from some sources. These look like long 9mm. I can't remember what the stamp was.
I look at every case anymore. Its the only way!!
Rolling Stone