Database

db={"percentages":[{"_id":1,"base":"A","buy":"BUY_1","sell":"SELL_1","item":"ITEM_B","ask":100,"bid":114,"percentage":14},{"_id":2,"base":"B","buy":"BUY_2","sell":"SELL_2","item":"ITEM_G","ask":50,"bid":90,"percentage":80},{"_id":3,"base":"A","buy":"BUY_2","sell":"SELL_2","item":"ITEM_G","ask":10,"bid":15,"percentage":50}],"discardeditems":[{"_id":1,"buy":"BUY_1","sell":"SELL_1","item":"ITEM_B"},{"_id":2,"buy":"BUY_2","sell":"SELL_2","item":"ITEM_G"}],"filtereditems":[{"_id":2,"buy":"BUY_2","sell":"SELL_2","item":"ITEM_G","percentage":"55"}]}

Query

db.percentages.aggregate([{$lookup:{from:"discardeditems",let:{item_src:"$item",buy_src:"$buy",sell_src:"$sell"},pipeline:[{$match:{$expr:{$and:[{$eq:["$$item_src","$item"]},{$eq:["$$buy_src","$buy"]},{$eq:["$$sell_src","$sell"]},]}}}],as:"discarded"}},{$lookup:{from:"filtereditems",let:{item_src:"$item",buy_src:"$buy",sell_src:"$sell",percentage_src:"$percentage"},pipeline:[{$match:{$expr:{$and:[{$eq:["$$item_src","$item"]},{$eq:["$$buy_src","$buy"]},{$eq:["$$sell_src","$sell"]},{$lt:["$$percentage_src",{$toInt:"$percentage"}]}]}}}],as:"filtered"}},{$match:{filtered:{$eq:[]}}},{$addFields:{isdiscarded:{$gt:[{$size:"$discarded"},0]}}},{$project:{discarded:0,filtered:0}}])

Result