Bug 1 is that Quicken updates balances without properly clearing transactions producing an artificial low balance that has been discussed elsewhere.
Bug 2 is that when this occurs, the website shows a negative balance but the warning email SHOWS POSITIVE BALANCE of the same amount.
It takes some detective work between my bank site and Quicken to figure this out manually. I pay for Quicken to figure this out for me. And not tell me I'm overdrawn when I'm not (Bug 1). But at least be internally consistent.
[edited title for clarity]