If the game won't deselect a spell, it's probably because it's coming to you from a different source - in the case of a Wizard, you might be getting it from an item - such as Rain Dancer giving you Create Water, or the Blasting Circlet giving you Scorching Ray. In the case of Clerics, your domain spells will be the same.
The game fails to make this clear, but ones that you have access to which are not counting against the number you can prepare will not have a white border on them, even though they are lit up in the spell book.
In any case, I do hope they allow wizards to learn from scrolls in the new patch like the game says they can.
Right now the issue, rather is that they can do this too much - and have been able to since the Ea release. Wizards can scribe any spell, regardless of whose list it is on. This means wizards with cleric spells, wizards scribing new cantrips (which is a fallacy since cantrips are not recorded in your spell book at all), and other similar shenanigans. At the same time, they've also allowed literally anyone to use spell scrolls as well. This is another case where they've made a change from the base rules without any real understanding of the balance and repercussions, though much feedback has been provided on the issue, and hopes are high that they'll reconsider and fix it.