I'd have to go back and rewatch it again, but here might be a few possible solutions;

(though it's been a looong time since I last watched it iwi)

• Most of the numbered agents didn't know eachother's faces until actually meeting eachother, and had not even seen "Mr.0" in person, so might have been likely that Croc just didn't give a sh#t who his underlings were.

• Robin may have been in charge of the hiring process and knew about Vivi, but just didn't bother to tell Croc.

• Croc might have known all along, but out of typical evil villainy, thought, "struggle all you want, it's futile," and just kept Vivi in his employment out of amusement.

• Disguises in One Piece really do go a long way..... though I highly doubt that Croc (being one of the 'smarter' characters) would fall for such a simple disguise, it could have been true.

Croco doenst meet his underlines personally hahaha