What is likely happening is that as the fired case is being squeezed down (in diameter) by the die, the case is actually getting longer until the shoulder is pushed back down by the die.
I suspect that you aren't adjusting the die down far enough. Another .002-.003" can make a big difference. However, if you already have firm contact between the shell holder and the die, you will need to grind/shorten the top of the shell holder a few thousands so that the die can be lowered slightly. You could, alternatively, shorten the die but why risk damaging the die which is hardened.
The shoulder dent is classic for excess lube. Only put enough lube on the case to prevent sticking. Many shooters do not put any lube on the shoulder itself.