The first phase of dropDatabase (for replicate sets) in 3.6 is to individually drop each collection (drop in this first phase is a misnomer for rename). When those "drops" are majority confirmed, the primary replicates a dropDatabase oplog entry.

However the loop uses an iterator over the _collections map and db->dropCollectionEvenIfSystem will perform a rename. This rename erases the entry followed by adding it back under a different name. The expectation of the for-each collection loop is that all collections will be observed. The erase/add of the underlying map breaks that requirement.

This can result in some collections not being dropped on the primary nor the secondary in the first part of dropping a database. I do believe the second phase of dropping a database that's associated with the dropDatabase oplog entry will be renamed and/or dropped on both the primary and secondary.

One possible fix is to copy the values from the map to iterate over instead.