Have you had an unclean shutdown on some of your nodes? You may be running into SERVER-19472, where an unclean shutdown may cause an incorrect count results using WiredTiger. Note that this is not a bug. The incorrect count was a direct result of an unclean shutdown.
You could try to:
Restart the affected Secondaries as a standalone node (without the --replSet parameter)
Execute db.collection.validate(true) on the affected collections
Restart the node with the --replSet parameter
Check if the count returned is correct once the node rejoins the replica set as a Secondary