An engine control system of a vehicle includes a cylinder control module a first air per cylinder (APC) module, an adjustment module, and a fuel control module. The cylinder control module determines a target fraction of activated cylinders of an engine. The first APC module determines a first APC value based on an intake manifold pressure and an air temperature. The adjustment module determines an APC adjustment value based on the target fraction of activated cylinders. The first APC module also determines a second APC value based on the first APC value and the APC adjustment value. The fuel control module controls fuel injection based on the second APC value and a target air/fuel mixture.