The first time Roxanne calls the crocodiles alligators it's an honest mistake.
It's the first time Megamind has her dangling over them, and the only thing she really notices about the teeth and jaws is the fact they're snapping at her oh god that's a lot of teeth—
But she is not going to let Megamind see that she's actually a little worried, this time—and besides, they aren't close enough to get to her; she does see that, now—so she pulls herself together and says—
"Alligators. Wow."
—in as bored and unimpressed a tone as she can manage.
There's a little pause in which Megamind doesn't answer right away, and then he launches into a monologue about how deadly and hungry the alligators are, and how great the peril she's in is, blah blah blah.
It's only seven months later, after he's already menaced her with the 'alligators' several more times, that she realizes they are, in fact, crocodiles.
She's watching a late-night documentary on the nature channel, and the host explains how to tell the difference between alligators and crocodiles based on their respective jaw and teeth shapes, and that it's crocodiles who exhibit the characteristic lunging and snapping behavior of active predation versus the still and quiet ambush predation of alligators and oh wow, now she feels like a complete and utter idiot.
Except—except Megamind calls them alligators.
Does he—does he actually not know? He's incredibly brilliant, but—simple things sometimes escape him, like the way he'll habitually mispronounce words or mix up idioms, and she knows that some of that is on purpose but she can tell some of it is genuine, too.
It's—it's possible that he doesn't know.
The next time he has her hanging over them, he calls them alligators and there's a split second where Roxanne thinks about correcting him, but—well, it just seems unnecessarily mean, really, like mocking the way he talks would be. She points out the mistakes in his machines, in his plans, yes, but—correcting him on this just seems petty and cruel.
So she doesn't do it.
(by the time he brings them out to 'threaten' her again, she's constructed an elaborate bit of technobabble about specially trained and genetically altered alligators made to exhibit vicious attack predation behavior, in case someone else ever brings it up to her. Another journalist does, once, at a conference, and Roxanne tells the lie with all the confidence of Megamind himself, giving an evil monologue, until the other journalist is nodding along, as though the explanation makes perfect sense.)
The first time Roxanne calls the crocodiles alligators, Megamind goes to correct her, goes to explain the differences between crocodiles and alligators, how you can tell them apart, how—
—but then—he stops.
He and Miss Ritchi's regular battles of wits are intense, yes, but there are still rules—standards—limits.
She never mocks his difficulties with certain words and idiomatic phrases. He knows she could easily make him sound stupid with that, if she tried, if she pointed out the so-simple things that cause him so much hardship. But she doesn't do that, not ever. It's very—chivalrous of her, really, very gallant. He appreciates it a great deal.
And so the idea of him using her little mistake about the crocodiles against her, to make her feel stupid, seems—cheap. A nasty bit of easy mockery.
A villain may be cruel, but he should never be mean.
So he doesn't correct her.
He doesn't correct her that time, or the next time, or any of the times after that, and pretty soon he's in too deep; he's calling them alligators, too, to other people, not just to her, ready to lie through his teeth and insist that they're alligators and not crocodiles to anyone who asks, ready to swear it before biologists and wildlife experts and god himself if need be.
(When one of the city's other villains points out, sneeringly, that the reptiles he owns are crocodiles and not alligators, based on 'certain easily observable characteristics', Megamind flashes him a dangerous smile and offers to toss him in their enclosure and let him observe them more closely, in the interest of scientific accuracy, and the man goes pale and backs down immediately, stammering apologies about how he must have been mistaken.)
(It is several years into the elaborate dual crocodile/alligator deception—and several months into their romantic relationship—before Megamind and Roxanne figure out that they are both, in fact, actually aware that the 'alligators' are really crocodiles, and that they've both been covering for each other unnecessarily all this time.)
notes: inspired by discussions on tumblr about Megamind's alligators with various fandom members, including displacerghost, joanhello, and ladyspock7. The plot point of Roxanne telling the other journalist about the 'specially trained alligators' was inspired by a comment by Oliver2016.