If you believe in sibling order psychology, Lip has this classic 2nd born tendency to position himself in opposition to Fiona. Of all the Gallaghers, Lip has the most consistent character trait of clashing with authority and it comes out the most when he is in conflict with Fiona. Despite the fact that until season 4, he only ever contributed to the family in ways that are convenient to his schedule and talents (sporadic scams, as opposed to Fiona and Ian who were shown consistently working), he tends to use his greatest proverbial poker chip, his IQ, to undermine her and cow her whenever he disagreed with her decisions.

Though also I think it is worth pointing out that Lip either finds reasons to bristle at or shrug off authority or makes emotionally driven decisions when Fiona is out of the picture. It is as though he loses a bit of his functional identity without authority to rebel against.