You're welcome! There does not appear to be anything wrong with the original fillets, I think it is a bug in boolean union between fillets when one of them has an extended "underlying surface" that goes a ways past the current trim boundaries and the second one is contained inside that extended underlying surface area.

I've been seeing the after effects of this bug for quite a while now but I didn't have a good way to reproduce it but I do now with your file. That should give me a good chance at fixing it.

- Michael