Mongo shell not creating indexes on running databases - mongodb

Question

We dumped the definition of indexes using mongo-index-exporter and we try to apply them at each launch of our application, so to achieve a reproducible environment, by executing
mongo --verbose "mongodb://$MONGO_DB_USER:$MONGO_DB_PASSWORD#$MONGO_DB_HOST/$MONGO_DB_NAME?authSource=$MONGO_AUTH_SOURCE&authMode=scram-sha1" indexes.js
on a file like so:
print('Using db ' + db)
setVerboseShell(true)
print('Creating indexes on mycoll1')
db.mycoll1.createIndex({"_id":1}, {"name":"_id_", "background": true});
db.mycoll1.createIndex({"createdAt":1,"field1.field2.field3":1}, {"name":"coll1_field123_idx"});
print('Creating indexes on mycoll2')
db.mycoll2.createIndex({"_id":1}, {"name":"_id_", "background": true});
db.mycoll2.createIndex({"createdAt":1,"field1.field2.field3":1}, {"name":"coll1_field123_idx"});
To create indexes on a replicaSet with five nodes, we are performing the
following command:
mongo --verbose "mongodb://$MONGO_DB_USER:$MONGO_DB_PASSWORD#$MONGO_DB_HOST/$MONGO_DB_NAME?authSource=$MONGO_AUTH_SOURCE&authMode=scram-sha1" indexes.js
this works fine for us in QA, where MONGO_DB_HOST is a single node and we are using a fresh new empty database, and doesn't work in production where additionally the database is already existing (and the collection have contents).
Additional relevant information:
background mode doesn't make any difference
The verbose mode doesn't work, i.e. although we launch mongo client with -v and we do a setVerbose(true) nothing is logged on the console
Our mongo shell is 3.6.11 and our mongo server is 3.2.9
Copy pastying the commands inside a mongo shell executed on the server works terminates immediately and results in the following output
{
"createdCollectionAutomatically" : false,
"numIndexesBefore" : 11,
"numIndexesAfter" : 11,
"note" : "all indexes already exist",
"ok" : 1
}