When testing mongorestore with an oplog, I see a lot of these in the log when testing against 3.6-rc4.

2017-11-19T06:13:07.386-0500 D -        [conn15] User Assertion: 226:cannot apply an op with a timestamp in atomic applyOps mode; will retry without atomicity src/mongo/db/repl/apply_ops.cpp 194

The applyOps command is then retried without "atomic" mode and succeeds, so the main effect so far appear to be log clutter.

milkie believes we should just remove timestamps. (I wonder if we should do that in mongodump rather than in mongorestore.) benety.goh points out that there is also an undocumented option to turn off atomic updates. geert.bosch believes either should be fine.