CUPID-Mo is a cryogenic detector array designed to search for neutrinoless double-beta decay ($0 ubetabeta$) of $^{100}$Mo. It uses 20 scintillating $^{100}$Mo-enriched Li$_2$MoO$_4$ bolometers instrumented with Ge light detectors to perform active suppression of $alpha$ backgrounds, drastically reducing the expected background in the $0 ubetabeta$ signal region. As a result, pileup events and small detector instabilities that mimic normal signals become non-negligible potential backgrounds. These types of events can in principle be eliminated based on their signal shapes, which are different from those of regular bolometric pulses. We show that a purely data-driven principal component analysis based approach is able to filter out these anomalous events, without the aid of detector response simulations.