Stability of orbital resonance
I am not very familiar with orbital dynamics (so please correct me if I'm wrong). I was told that, for instance in the case of the mean motion resonances that cause the majority of the Kirkwood gaps in the asteroid belt, not only the ratio of the periods, but also the timing is important. 

Let's take Pluto as an example, which is in 2:3 resonance with Neptune. Although Pluto crosses Neptune's orbit, both bodies will never get closer to each other than a certain threshold. That is, because the timing between their orbits was preventing close encounters in the first place, which is then enforced by the resonance. 

If the timing was different, close encounters would be possible, thus destabilizing the orbit of the smaller body. In the case of mean motion resonances, there is an algebraic expression that allows to investigate the stability of a resonance (see, e.g., here https://en.wikipedia.org/wiki/Resonant_trans-Neptunian_object [toward a formal definition]).