I've had this happen before, and it was due to conflicts between installed packages and the new repos. If you try to run the upgrade through command line, it will let you know if it comes across any issues while trying to upgrade. In my case (I think this happened to me on Fedora 37, maybe it was 38 though), I believe I had some Python package installed that wasn't in the new repo, so it stopped my upgrade, and I had to use the --allowerasing flag on the command line upgrade to fix it.

The other user linked to the appropriate docs for using the DNF System Upgrade plugin, but I would like to point out that the docs specifiy that upgrades are tested from the 2 previous releases (meaning that you should be able to skip from Fedora 38 to Fedora 40 without installing Fedora 39). So you should be good to upgrade straight to Fedora 40 with a single dnf system-upgrade. Read the output carefully, and if it suggests to use the --allowerasing option, review the incompatible packages (I recommend writing them down if they are important), and then rerun the command with --allowerasing. I strongly discourage running a dnf system-upgrade with --allowerasing before you know what packages it may erase.