If it's just the Federal cases with the internal step that are bulging, then I think that's your problem. Segregate them out from the rest.
The bulging may not be a problem if you use a Lee Factory Crimp die as your last step. It will post size each round and should remove the bulge. Not elegant but satisfactory.
You might also try a different flare die, like the Lyman M die. It may be able to flare the case without getting so far down into the case that it hits the internal step. I also doubt that the Lee Pro Auto Disk powder-through expander die will get that far down into the case, but I'll have to check.
You've got me a little concerned now, because I've been shooting up a case of Federal .380 Auto I purchased a couple of years ago planning on reusing the brass. If that Federal brass with the internal step is going to cause me trouble reloading, I might have to make different plans.