Some run-out is to be expected in bullet seating. The important thing is to keep it to a minimum. Serious run-out is often caused by using the incorrect seating stem for the type of bullet being used. It is also caused by failure to keep the die and all of its parts clean. Even my Redding competition dies need to be handled with love and affection.
Uneven pressure at any point in the seating process will cause run-out so it is often a good idea to seat the bullet only a few thousandths, turn the case 180 degrees, and seat it fully. Sometimes the run-out at seating is actually the fault of a poorly sized neck.