i have been running silverblue for about half a year now, and rely heavily on them.
i can remember 3 distinct issues:
vs code commandlines start in the sandbox, which needs a workarround (rather understandable)
either the fedora, or the flathub build of firefox didnt come with some video codec, OpenH264 i think. switching to the other build fixed it (imo more a licensing issue with the codec than a flatpak problem)
on rare occasions (about once every 3 month)
steam behaves weirdly, and refuses to start until i update the flatpak.