And the money withdrawn from PayPal account to bank account.
And realizing that my credit card bill that's due Feb 2nd was paid a month ago.
This is my biggest issue with them: bill payments. They don't match up bill reminders with transactions. So, as you said, something you've paid still shows up as due and once the due date goes by, if you haven't paid it, it just disappears off your list even though it's still outstanding. They really need to fix this.
Is your savings account tracked by mint? Because I do this all the time and I don't see it listed as income, it's a transfer.
Maybe it depends on specifics. Mint must have some heuristics that attempt to discern whether or not a transaction is a symmetric internal transfer and they work for some and not for others. It's not an easy problem, given the zillion variables and different banks etc. but after all these years and witnessing the choices they've made on where to allocate resources it's hard to give them the benefit of the doubt.
If you keep categorizing transaction from, say, checking to credit card or savings to checking as transfers it'll pick up on it after a bit and automatically categorize them.