Not sure what her financial situation is, but if the loan on her car was the oldest thing on her credit report paying it off will lower the average age of her credit history and that can lower your score.
If she had a credit card that was opened before she got the car loan and never missed a payment on the credit card, paying of the car would have raised her average credit history and raised her score.
It's not some secret how this stuff works, Credit Karma tells you all this.
you misunderstand the function of the score. it's not a score that tracks how reliably you pay back your debts, it's a score that tracks how profitable you are as a debtor. someone who pays it all back before masses of interest can accumulate is not profitable. someone who doesn't pay it back and drowns in the interest is also not profitable. the best scores are for the people in between, who make the creditors lots and lots of money consistently.
It's for this reason that "building credit" over time is ridiculously easy if you game it properly - it's basically pay to win. the more consistently you pay interest but without looking like you're drowning, the happier they are. it's why having some utilization gets you better scores than paying everything off completely and having 0 utilization every month.
i agree it's very stupid in terms of incentivization and think it's probably the worst measure of social value we could have arrived at.