Some institutions Mint is able to interface with more easily, and some less easily. Let's face it, banks have some of the most outdated technology stacks still being actively used -- that's why lots of them restrict your password to no more than 12 characters, no punctuation, etc, even though it's less secure, because they have compatibility issues with some of their old systems/software.
I have go so far as to actually switch banks because Mint wasn't able to reliably keep the account up to date. Yes, I actually did that, I switched banks for that one reason. Of course, not everyone can do that, a checking account is one thing but when you're talking about retirement accounts et al, they are where they are and often aren't easily moved.