Well, he ALREADY said something he would regret a big time... Some evil forbidden wish.
No. He meant possibly his mother would be alive if he didn't try to save her (It's more correct to say "Then my mother would be with me"). Cera saved them all only at the end. Other times, she... constantly went the wrong way.
As you rememeber, in original movie, going the wrong way is Cera's element.

Literally. Including their first meeting with Sharptooth, where Littlefoot saved her at least three times in small scenes.
He's evilly mad at Cera for particular action, or words... Something broke our lovely longneck so he dared to say such cruel evil words he couldn't ever say even in original movie. And his act broke Cera's strong-will, making her cry.
Who knows, this scene can happen anytime, not just in past days...
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Thank you!