We have theoretically studied how resonant spin wave modes in an elliptical nanomagnet are affected by fabrication defects, such as small local thickness variations. Our results indicate that defects of this nature, which can easily result from the fabrication process, or are sometimes deliberately introduced during the fabrication process, will significantly alter the frequencies, magnetic field dependence of the frequencies, and the power and phase profiles of the resonant spin wave modes. They can also spawn new resonant modes and quench existing ones. All this has important ramifications for multi-device circuits based on spin waves, such as phase locked oscillators for neuromorphic computing, where the device-to-device variability caused by defects can be inhibitory.