Since we no longer take a DB MODE_X lock for collMod (see SERVER-46865), the code for resolving namespaces in aggregate(), which takes a DB MODE_IS lock, does not necessarily see a consistent "view" of the view catalog. See link.

This means that aggregate() can execute a pipeline on a set of view definitions that are not valid/nonsensical and possibly even contain a cycle.

One potential fix would be to have the view resolution in run_aggregate be performed while holding a collection IS lock on system.views. I believe this will fix the issue as long as collMod continues taking a collection X lock (see here).