I tried to create a minimal reproduction case in that repo: https://github.com/davinov/mongo-5-query-segfault If you have 2 collections: first collection `data_1` with two docs: [{ "Identifier" : "K4" }, { "Identifier" : "K8" }] second collection `data_2` with one doc: [{ "Identifier" : "K4" }] and execute the following aggregation: db.data_1.aggregate([ { "$lookup" : { "as" : "_lookedUp" , "from" : "data_2" , "pipeline" : [ { "$group" : { "_id" : { "Identifier" : "$Identifier" } } }, { "$facet" : { "data_2" : [] } } ] } } ]) In mongo 4, this works as expected, the result being: [{ '_id' : ObjectId(), 'Identifier' : 'K4' , '_lookedUp' : [{ 'data_2' : [{ '_id' : { 'Identifier' : 'K4' }}]}]}, { '_id' : ObjectId(), 'Identifier' : 'K8' , '_lookedUp' : [{ 'data_2' : [{ '_id' : { 'Identifier' : 'K4' }}]}]}] In mongo 5, the server crashes with the following logs: '{"t":{"$date":"2021-10-12T10:29:42.544+00:00"},"s":"F", "c":"CONTROL", "id":4757800, "ctx":"conn4","msg":"Writing fatal 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