Aquillion

I've noticed that if I read a book or use a canister that teaches a skill, spell, or shaped creature, then try to increase it at a trainer, the point I gained from the book/canister counts against the two points I can gain from training; I can only increase the skill to a total of 2, and (assuming I used the only book/canister available to me before training) can apparently never raise the spell/shaped creature above 2. But, if I train two times from the trainer first, I can still use the book/canister, resulting in a total of 3. Is this a bug, and if so, which case is bugged? And, perhaps more importantly, is my character permanently crippled if I train from a book or canister before using a trainer?