Ken, I haven't had as much experience as you might think with PE parts, but yes, I have found that sometimes they don't fit as they should or as I might want them to. Sometimes the instuctions are too vague and I can't determine just how a part should be placed.
On problem I discovered is that adding a PE part changes the dimensions of a kit part. An example of this is the seats on the Hornet: there were sides to be added and when I went to install them, they no longer fit into the cockpit tub. I should have realized this and thinned the seats a bit to allow for this. I ended up grinding the sides of the tub to make them fit. As it was, I pondered whether these parts were needed as they are now fully hidden from sight!
I know I am going to have to watch for this:
The parts at the center of the photo are rings that get mounted on the edges of the canopy and the windscreen. I'm going to need to remove that much material from both if the cockpit is to be closed, otherwise it wouldn't fit. I suppose they could be left off if I choose to close everything up, but still I wouldn't have the mirrors that would show even with the canopy closed.
It's bad enough that the kit parts don't ever fit as they should, we choose to add to our frustration by trying add extra parts to the mix.
I often wonder how PE sets are produced. Many times it seems the aftermarket parts are hitting the market before the actual kits. I assume that there is a co-operation between Kit manufactures and someone like Eduard. They must send them pre-release examples like they would for FSM reviews.