Given a group cocycle on a finitely aligned left cancellative small category (LCSC) we investigate the associated skew product category and its Cuntz-Krieger algebra, which we describe as the crossed product of the Cuntz-Krieger algebra of the original category by an induced coaction of the group. We use our results to study Cuntz-Krieger algebras arising from free actions of groups on finitely aligned LCSCs, and to construct coactions of groups on Exel-Pardo algebras. Finally we discuss the universal group of a small category and connectedness of skew product categories.