There are a couple of reasons to actively prevent autofill passwords. The only one I have seen for login autofill prevention is when the password is actually a generated token (ala yubikey,etc) and a password manager won't do the right thing by default.

There are regulatory bodies that require regular challenge of user identity for approving items as sort of a signature mechanism. This is another time where active thwarting the password manager makes sense. Whether or not the regulation makes sense is an entirely different issue.