Robomongo : Exceeded memory limit for $group

{ allowDiskUse: true } 

Should be placed right after the aggregation pipeline.

In your code this should go like this:

db.getCollection('RAW_COLLECTION').aggregate([
  // Group on unique value storing _id values to array and count 
  { "$group": {
    "_id": { RegisterNumber: "$RegisterNumber", Region: "$Region" },
    "ids": { "$push": "$_id" },
    "count": { "$sum": 1 }      
  }},
  // Only return things that matched more than once. i.e a duplicate
  { "$match": { "count": { "$gt": 1 } } }
], { allowDiskUse: true } )

Note: Using { allowDiskUse: true } may introduce issues related to performance as aggregation pipeline will access data from temporary files on disk. Also depends on disk performance and the size of your working set. Test performance for your use case