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We consider linear and nonlinear transport equations with irregular velocity fields, motivated by models coming from mean field games. The velocity fields are assumed to increase in each coordinate, and the divergence therefore fails to be absolutely continuous with respect to the Lebesgue measure in general. For such velocity fields, the well-posedness of first- and second-order linear transport equations in Lebesgue spaces is established, as well as the existence and uniqueness of regular ODE and SDE Lagrangian flows. These results are then applied to the study of certain nonconservative, nonlinear systems of transport type, which are used to model mean field games in a finite state space. A notion of weak solution is identified for which unique minimal and maximal solutions exist, which do not coincide in general. A selection-by-noise result is established for a relevant example to demonstrate that different types of noise can select any of the admissible solutions in the vanishing noise limit.