I prepared Cure Wounds by clicking on the spell in a 2nd level slot and it disabled Cure Wounds in the 1st level slot.
Casters should simply prepare spells without regard to slots. Cure Wounds, if prepared, should be available from 1st level slots and any higher slot.
A more straightforward UI would just have a list of know spells from which the player indicates which are prepared. Slots are irrelevant for preparation.
The same UI should also indicate spells that are always prepared (i.e. due to subclass) separately so the player understands why those don't need to be prepared.
The existing UI is confusing even for someone who knows 5e.
The way it is done now brings me not so good memories about preparing spells in 3.5, when you had to choose how many casts of one spell did you wanted. When you select a spell, you should be able to choose in which level do you want to cast it. Maybe just clicking one of the rectangles that displays your number of slots, to select the level, and then select the spell.
And the tool bar for spells and abilities feels really tiny. Having to cycle between different ones is not something that I find enjoyable.
The way Larian have it currently working is this:
Spells which have an upcast capacity appear in every spell level. If you have memorized it at 1st level a cure wounds will show up at 2nd/3rd etc.
Spells which are upcast versions have the roman numerals in the bottom right corner to denote this. So Cure wounds at 2nd level is the same as 1st, but has roman numerals showing on it. Prayer of Healing, only available from 2nd, shows up without them.
If you went to learn cure wounds 2nd level after having already learned it at 1st, you are turning it off for both because it's the same spell and linked correctly.
I don't disagree that it is confusing, but once you learn it it's very straightforward - just look for the roman numerals (the I II III IV etc) on the icon to realise that is a 'free' button, since the spell still only counts as being 1 memorization for the 2 buttons).
The problem here arise in that, if I'm not mistaken, that 2nd level Cure Wounds still counts against the number of spells you can prepare. That way, you are limiting your spell selection just to have Cure Wounds at both first and second level, taking two slots when it should only take one. Maybe I'm mistaken, didn't messed a lot with it. If I'm wrong, feel free to correct me.