This has started happening since the latest patch: When I try to prepare my cleric spells after a long rest, everything in the spell preparation UI seems to be working as intended and I am able to select the desired spells. After the rest is complete however, the spells available are the ones that appear as default before I started changing them. (In my case it's really easy to notice as the defaults always include detect evil and bane, which I never take).
This did not happen before the latest patch (playing my second playthrough after patch came out).
Side-note: I find it very silly that the game does not persist the choices I had made previously and use those choices as the default ones in subsequent rests.