Well the thing is we know very little about Cora and Queen of Hearts on this show. So it could be the same person.
I guess Regina could have lied to Jefferson saying Queen of Hearts considered her a threat for if she's her mother she would be trying to reel her in. The only problem I have is how Cora ended up in Wonderland and became their queen. So far there's only three ways of leaving Fairy Tale World. Jefferson's hat, magic beans, and Rumple's curse. But Jefferson had his hat and The Blue Fairy said the rest of the magic beans were gone before Cora was born. I guess she could have found one of the magic beans or used another way to Wonderland we don't know about yet.