So far I have not had any glitches preparing spells but there are a few things to take note of. First, cantrips are never prepared but instead picked so they will never have to option to prepare them when clicking the Prepare Spells button. Second, if you are a Cleric, your Domain spells are always prepared BUT they appear to be greyed out so its easy to confuse them with not being prepared. You should still see them available to cast. As everyone else said, the only time you can prepare spells is after a Long Rest and clicking the button.
Now semi-related, when I leveled to 3 and was picking spells for my Wizard to learn, I didn't notice the Level 2 spells so I picked Level 1 spells instead. Level two was just further to the right and I missed it like a dummy but there are some short cuts near the bottom of the screen (C I II) that if you click on it would take you to that level of spell to more easily pick spells for that level.
Hopefully that prevents someone else from making the same mistake.