[{"_id":1,"item":{"code":"ABC1",skus:[" c1","c2","c3"]}},{"_id":2,"item":{"code":"ABC2",skus:["c1","c2","d 3"]}},{"_id":3,"item":{"code":"ABC3",skus:["d1","d2","c3"]}}]

db.collection.find({$expr:{$ne:[{$setIntersection:[{$map:{input:"$item.skus",in:{$replaceAll:{input:"$$this",find:" ",replacement:""}}}},["c1","d3"]]},[]]}})