Any idea what is causing this? It can sometimes be far more dramatic, where the rogue waypoint sends them completely off of the terrain. 
After reviewing this post…
RadiusModifier paths into unpathable space - General - Support Forum (arongranberg.com)
It sounds like Funnel and Advanced Smoothing can cause an issue if on the same agent. I removed Advanced Smoothing and the problem went away.
I hope this helps someone else at some point. 
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