If your 650 is skipping primers are they ending up in the "ski-jump" that collects primers not inserted? If so, two possible problems. First is the small lever that holds the case in the shell plate at Station #2 is not adjusted properly. The lever should have no more than about .002" of clearance between it and the case when in this station. Adjust it with the small set screw in the casting that holds the lever.
The second possibility is that you are not fully pushing the lever forward to seat the primer. Improper adjustment of the case positioning lever in station 2 will cause the operator to feel resistance and think the primer is seated, when in actuality it is not. This also causes the press to not fully insert the case in Station #1, that is if the mechanism is properly adjusted.
Go back to the setup instructions and adjust the mechanism for Station #1 and Station #2 Page 38,39 Figs 188 through 195.
You'll be amazed at how smooth things will go if these adjustments (which Dillon hid in the back of the manual) are correct.
No, I don't work for Dillon, I just had to learn this from experience like others.