I'm sure that the great majority of cases of bots getting stuck are due to deficiencies in the navmesh. I let marauder bots play for a few minutes on parpax and observed them getting stuck in two places visible in this screenshot below: atop the spherical structure on the left, and on the group of three boxes on the right. In both cases, the navmesh at least visually appears to be disconnected. This is not always the case though; in another room a bot got stuck in a place where the mesh was not visually disconnected.
However, I'm not sure about the fidelity of this visual representation of the navmesh (displayed by navedit enable level2); there is no guarantee that the apparent disconnection exists in the internal graph representation.
Places where bots can be stuck without navmesh deficiencies also exist. For example, exiting from the depicted human base to the right, there are some shallow holes which human bots can fall into.
I do believe that deleting the bad parts of the navmesh would help the problem. I think there is code for bots to try to get back onto the navmesh when they are off it. Unfortunately, in the presence of deficiencies this can make things worse: I've seen bots deliberately going back to the disconnected part of the mash after they have managed to get off it using the unstick procedure.