A variety of methods and arrangements for detecting failure of the commanded air induction in an internal combustion engine are described. In some embodiments, the intake manifold pressure is monitored. An air induction event generates a fluctuation in the intake manifold pressure, which is recorded. The signal is processed through a diagnostic filter to help determine whether the actual induction matched the commanded induction. In other embodiments, measured crankshaft acceleration is compared with estimated crankshaft acceleration. If the two quantities differ by a threshold amount an induction fault is detected. The two detection methods may also be combined. The describe approaches are particularly well suited for use in engines operating in a skip fire mode with cylinder deactivation and/or a dynamic firing level modulation mode.