Database
[{payments:[{total:51},{total:52},],},{payments:[{total:50},{total:50},]},{payments:[{total:0},{total:50},],}]
Query
db.collection.aggregate([{$project:{payments:"$payments",paymentsGreaterThanZero:{$size:{$filter:{input:"$payments",as:"item",cond:{$gt:["$$item.total",0]}}}}}},{$match:{paymentsGreaterThanZero:{$gt:1}}},{$project:{payments:"$payments"}}])