Had, Nick didn't miss the past tense there and he also didn't miss the my but he chose to ignore the latter and accept that Stark did at least sort of understand and Nick didn't have to hear him admit it. What he did have to do, apparently, was offer Tony some kind of assurance and it was a weird reminder of the kid he'd met all those years ago, the kid at Howard's funeral and the kid Nick was always fishing out of trouble and who maybe just needed a pat on the back every now and then. Stark was probably always going to be that kid and since Nick was apparently everybody's daddy he could reassure him now. Maybe with a little positive reinforcement he'd get off his moral high horse about this and stop being such a judgmental asshole. Fury didn't even mind that much; he'd had to defend himself against more righteous motherfuckers than Tony Stark plenty of times.
"You've always had my back," Nick agreed easily and added, "And I've always had yours. But you've got a lot of backs to look after, Stark, and when shit hits the fan you've got your own problems to worry about. Pretty sure you can get yourself into enough trouble without tangling yourself up in all my shit, too."