Or... Ivankov is just simply the one that gave Crocodile his scar...
Thank you. Ever since genderbender-Iva turned up, if he so much at looks at someone funny it's assumed they must have been a female in the past. Wait for the big reveal where Dragon is actually Luffy's mother!
In all seriousness, what Iva knows about Croc has a high chance (read: 95%) of being related to the scar on his face, and the hand that he's missing. If you remember Chapter 0, Croc's face was hidden. Let's name another famous pirate with a scar who keeps having his face hidden in flashbacks: Shanks!
It's almost an Oda-trend.
Don't think Iva gave Croc his scar. Most likely he simply knows about whatever the incident was that gave Croc his scar. If it was simply genderbending, do you think Croc would really even be worried about that? Iva never seemed to believe his gender bending was of any harm to anyone, but simply an upgrade. Iva's "upgrade" would not be seen as Croc's "weakness".