Resolved: ostree 2023.4-2 (as linked in the comments below) has been pushed to stable, updating your system will resolve the issue.
Tl;dr: There seems to be a bug in ostree-libs 2023.4 that causes errors when trying to update flatpaks, gnome software loads forever when trying to update a flatpak and manually running flatpak update shows errors (I was getting an "input buffer too small" error, others seemed to be getting errors like "Need more input".)
Running sudo dnf downgrade ostree worked perfectly for me, I'll be ignoring the ostree/ostree-libs update for now and hopefully the issue will be resolved soon.