Okay, I thought there was a bug because I acquired multiple spells across all of my playthroughs but have never been able to trigger them. Perhaps some sort of reactionary "This spell won't do anything at this time" or something might help, because I've never been able to get any to work. Anyways, interesting game! I'll try the spells again later.
I cannot reproduce this issue.
If you collect a spell you can press number keys 1, 2, or 3 to activate them. If they cannot be cast there is a noise and a red cross will appear over the spell. The numpad keys will be affected by numlock so you may want to use the main keyboard numbers.
Example: This is the randomise spell being cast by pressing the 1 number key.
