Nonpotential effects in nonlinear evolution of Marangoni convection patterns are investigated analytically and numerically. Three manifestations of nonpotential effects are considered: (i) spatial modulations of hexagonal patterns; (ii) interaction between a short-scale hexagonal pattern and a long-scale slow deformational (Goldstone) mode; (iii) generation of the mean flow by the free-surface deformation in a large-scale Marangoni convection with poorly conducting boundaries. Nonpotential effects are shown to cause various secondary instabilities leading to skewed hexagonal structures, coexisting u- and d-hexagons, oscillating hexagonal patterns, spatially irregular cellular patterns, etc.