This should have been the version fixing the issue. The troublesome version was 2023.4-1.
On my end:
pacman -Qi ostree
Name : ostree
Version : 2023.4-2
Description : Operating system and container binary deployment and upgrades
And I just had some flatpak updates that went fine:
ID Branch Op Remote Download
1. [✓] org.freedesktop.Platform.GL.default 21.08 u flathub 23.8 MB / 129.8 MB
2. [✓] org.freedesktop.Platform.Locale 21.08 u flathub 17.7 kB / 326.8 MB
3. [✓] org.gnome.Platform.Locale 44 u flathub 17.7 kB / 340.5 MB
4. [✓] org.gnome.Platform 44 u flathub 86.1 MB / 326.0 MB
5. [✓] org.freedesktop.Platform 21.08 u flathub 31.9 MB / 202.3 MB
See: Ostree 23.4.1 breaks flatpak installs and updates; fixed in 23.4-2 in extra-testing