mongorestore --drop sometimes reports duplicate ID violation restoring system.js

When trying to restore a database dumped with mongodump via mongorestore:

 mongorestore --drop --host localhost --db mydb mydumpdir\mydb 

I sometimes get:

ERROR: Error creating index mydb.system.js: 11000 err: "E11000 duplicate key error index: mydb.system.js.$id dup key: { : "myfunction" }"

This only happens on the second restore after a manual drop, i.e. if I manually drop the database and then restore it, it restores fine; a second restore would error out with a duplicate key error; but any subsequent invocation of the same restore command (without manual dropping) succeeds.