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).
