I'm guessing they'll have a big dramatic reveal with Valentine being Jace's father, but not Clary's, at least not yet if they plan any sequels. They may wait to make Clary's dramatic reveal until we know Valentine is lying or something.

See, in the book, it was bad enough that you had Valentine dramatically revealed as the father twice within two chapters of each other--you certainly can't do it in a movie, 'cause in a movie it would be condensed within minutes of each other.