In vapor cell atomic clocks the atom-field interaction is typically obtained inside a microwave cavity resonator in which the microwave driving field together with a static magnetic field and an optical field are applied to excite the atoms. These fields are generally well-controlled, mutually aligned to a common quantization axis. Since the exploited atomic transition is sensitive to any potential axis misalignment, the performance of the clock can also be affected. We study the effect of such misalignment for the case of a cylindrical cavity used in vapor-cell atomic clocks, taking into account the misalignments of the optical detection field and the static magnetic field required for the atomic transition. Both the geometry of the cavity and the factors contributing to losses can play role in the degradation of the signal and are taken into account in the misalignment problem discussed.