I upgraded and was charged a partial amount — why?

That's proration, and it's expected.

When you upgrade in the middle of a billing cycle, we charge only for the remaining days of your current period, at the new plan's rate. Then, on your next billing date, you're charged the full plan price as normal.

So a smaller-than-expected charge right after upgrading isn't a mistake — it's the prorated top-up that covers the rest of this cycle. See How does pricing work? for plan prices.