My API code is using the latest Mongoose 5.0.11 with the proper Mongo 3.4 connection string to connect to the free Atlas service.
mongodb://someadmin:
Seems that the user has no permission to listIndexes As per the documentation
Required Access The user executing the command requires either find privileges on the system.indexes collection or the listIndexes privilege action. At a minimum, the read built-in role provide the requisite permissions.
I accidentally removed the username from the connection string, so it only had password
where it should be username:password
which causes this error on any database.