I don't use these for my Kubes, but can totally understand your frustration. I had a peg lodged in one of my vintage figures and even though you couldn't see it on display, it drove me nuts. I had to eventually replace it because I'm OCD about that stuff. I don't have any idea how to fix it, but would love to hear suggestions if anyone has one.
With regards to the display cases, is that a common problem or an isolated issue? I can come up with complaints on just about every type of SW item I've run into, but sometimes you just have some bad luck on things like that. I use the JL cases for my figs and they stand up pretty well in there without the pegs. Probably not worth switching over all your stuff, but maybe it's worth not using the pegs on your future stuff if you're worried about this happening again.