I was checking the intelligence on Andolyrus vs how many books read and noticed the first number is lower than the second. This is unusual because I also remember buying intelligence points from the Spindle shop as well. I don't think I've zapped this pet back when the zapper decreased intelligence. I've also never kicked the gym vending machine.
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: I don't believe so.
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It's pretty well known doing anything on subeta at 00:00 can result in loss. Like reading books is no intel and when doing BQs it often eats the battle and won't acknowledge that you won and you'll have to battle the challenger again.
If I had to take a guess, that's probably what happened here (not that you'd remember a few months down the line, but... for future reference).
This happened to me and a few other users... quite a long time ago. Here is the thread, ended up getting patched up and the difference 'refunded', but there is no certain way of tracking what gains come from books and what gains come from boosters (so any intel there might be lost).