I've noticed roughly the same thing. Though I've never taken
measurements of the neck after resizing, if I'm using the ammo for anything but plinking, I trim the cases. I start with the shortest case and set the trimmer to take off just enough metal to make the end of the neck shiny all the way around then trim the rest of the cases to the same size.
I've noticed time and time again that the trimmer can bite on one side of the case and remove metal without taking metal off all the way around meaning that the case neck isn't perfectly square coming out of the resizing die. In other words, liek you said, the neck is being stretched unevenly.

I check all of the case lengths before trimming, if I find a case
that is slightly shorter or right at the minimum length before trimming, the case goes into my 'hodgepodge bin' to be loaded up as a plinking round.

Also, depending on the brand of die you use, the decapping pin can either be fixed as on a RCBS die or freefloating as on a Lee die. If it appears offcenter, and is a fixed type, I'm suprised it wouldn't break or jam since it might not want to aling with the flash hole while decapping. You might want to try replacing the pin to see if that makes a difference.

Alcohol, Tobacco, and Firearms... who's bringing the chips?