Shellholders, just like any other machined tool, will vary in size, as will brass. You might try another shellholder, if you have one. I try to keep several shellholders for all the calibers that I load on hand, just for this reason. The only problem is, they can also vary in height, which will affect headspace on bottleneck cases.
When you consider the millions of pieces of brass that are produced by the various manufacturers, in various countries, and using two different measuring systems, it's really amazing how close they are in tolerances. The same goes for tools.
The bottom line is, it depends on how bad you want to use the brass that is slightly out of spec in that one area. If it's worth the effort to you, then there are ways to do it, but if it isn't, then just scrap the brass.
Hope this helps.
Fred