A future alert had info on how to solve the issue - which in short is to download the mongodb logs and search for the inefficient query.
To download the logs
1. Navigate to the Cluster page
If you do not see the cluster you want on the page, ensure you have selected the > proper Project
2. Select the cluster
a. Click the ellipsis icon (...) next to the cluster containing the mongod instance whose logs you want to download.
b. Select Download Logs.
3. In the Download Logs modal, edit the following fields
Select process: Select the process for which you want logs. Valid options are mongod and mongod-audit-log.
Select server: Select the server in the cluster whose logs you want to retrieve.
Start Time: Specify the date and time in your group’s time zone defining the inclusive lower bound of log activity to return. The start time must be less than 30 days ago.
End Time: Specify the date and time in your group’s time zone defining the inclusive upper bound of log activity to return.
4. Click Download Logs
An inefficient query is explained here
The following mongod log entry shows statistics generated from an inefficient query:
planSummary: COLLSCAN keysExamined:0
docsExamined: 10000 cursorExhausted:1 numYields:234
nreturned:4 protocol:op_query 358ms<Timestamp> COMMAND <query>
This query scanned 10,000 documents and returned only 4 for a ratio of 2500, which is highly inefficient.