[{_id:"1234aaa",profile:{Organizations:["A","B","C","A","B","A"]}},{_id:"1234bbb",profile:{Organizations:["A","B","C"]}},{_id:"1234ccc",profile:{Organizations:["A","B","C","C"]}}]

db.collection.aggregate([{$addFields:{Dupes:{$filter:{input:{$setUnion:["$profile.Organizations"]},as:"s",cond:{$gt:[{$size:{$filter:{input:"$profile.Organizations",cond:{$eq:["$$this","$$s"]}}}},1]}}}}}])