Not sure, it doesn’t ring any bells. The way the size is calculated probably differs between the sources. One is likely not including all dependencies in its calculation.
For Flatpaks, Discover can only show what Flatpak is aware of itself. Providing accurate size estimates for updates is an outstanding item for that upstream project:
For Fedora packages, that information is coming from PackageKit, via its dnf backend. That backend, at least from the examples I’ve looked at on my system, seems to be providing the end-state installed size of the updated programs, rather than the size of the packages to be downloaded - presumably because of Install size versus download size in PkDetails by mcrha · Pull Request #476 · PackageKit/PackageKit · GitHub - see my example here:
For Fedora 41 and beyond, there’s likely to be some more work needed to either adapt the dnf PackageKit backend to fully work with DNF5, or to develop another plugin path for Discover to interact with DNF5 directly outside of PackageKit entirely - some discussion about that so far was had here: 480525 – Custom backend for DNF5