I would ensure that the connection is being made with the Mongo for BI connector 2.
It was released in 2017 and has some significant updates to 1.0. In the following blog post from the release there is some explanation to what might be occurring with the arrays that I have quoted below.
To transform this database into a form that a SQL-based tool can parse, we use the "mongodrdl" utility to create the mapping file.
Inspecting the output file will reveal that the nested arrays have been transformed into relational tables. Indeed, connecting to the file from the MySQL shell reveals the new schema:
Hope this helps!