During the initial sync process mongod will clone data from it's sync source via a getMore() operation. It is possible for this getMore to end early for a given collection on cursor invalidation, having returned only a partial data set. This results in a new replica member with an incomplete data set.

To trigger this issue the following must occur:
1) The cloner's getMore() is currently in progress on the sync source, in a yielded state
2) An index on the collection being cloned is dropped (either directly or due to a failed index build, one example being a unique index build that hits a duplicate key)

This does not appear to be an issue under 3.2.0-rc0.