Database

[{"_id":{"$oid":"6295d353fccb2f44c3868f9a"},"name":"test","managerid":{"$oid":"6295d353fccb2f44c3868f99"},"teachers":[],"employees":[{"employeeid":{"$oid":"6295d353fccb2f44c3868f99"},"firstname":"jean","lastname":"charles","tag":4595,"status":1}],"groups":[{"groupid":{"$oid":"6295fa2191ae50ba47e9d25c"},"groupname":"mongroupe","employees":[],"permissions":[]}]}]

Query

db.collection.update({"_id":{"$oid":"6295d353fccb2f44c3868f9a"},"groups.groupid":{"$oid":"6295fa2191ae50ba47e9d25c"}},[{"$set":{"groups.$.employees":{"$concatArrays":["$groups.$.employees",{"$filter":{"input":[{"employeeid":{"$oid":"6295d353fccb2f44c3868f99"}}],"cond":{"$not":{"$in":["$$this.employeeid","$groups.$.employees.employeeid"]}}}}]}}}])

Result