The gemara concludes that the entire mishna is discussing being yotzei yidei shamayim when the nifkad is claiming to have money of others but they are not making definitive claims against him (only ta'anas she'ma). Therefore, when one steals or receives a pikadon and should know how much he owes to each, when he doesn't know it is recommended that he fulfill his obligation to be yotzei yidei shamayim and repay each of them. But, when two people together handed him packages in a way where he is not expected to remember who gave what, when he can't recall who gave what, there isn't even a yotzei yidei shamayim requirement on him to pay back both. The Shulchan Aruch (c.m. 300:1) writes that when 2 people give a pikadon to a third, each giving different amounts, if each claims that he gave the higher amount he is actually obligated to fully repay each of them since he should have written their names on the packages. But if they are not making claims against him, rather he is approaching them and claiming that he has their money but not sure to whom he owes the higher amount (ta'anas she'ma), he is not obligated to pay them both the higher amount but should do so to be yotzei yidei shamayim. This is all assuming that they gave it to him separately, but if they handed it to him together in one bundle (or according to rashi at the same time is tantamount to one bundle) - in way where he isn't obligated to recall who gave what, even if each one claims the higher amount, he is not obligated to pay the higher amount to both. The rationale is that he can claim that when they originally gave it to him together, they indicated that they were not makpid on each other. Even to be yotzei yidei shamayim he is not required to pay both.
The ketzos raises a question from the Shulchan Aruch (222:2) who rules that if one purchases an item from a store and can't recall which store he purchased it from, he would be obligated to be yotzei yidei shamayim by paying each one of the 5 stores that he may have purchased from. Why is there a greater chiyuv to be yotzei yidei shamayim in that case? (The assumption is based on tosafos that in the case of the sale he is also not required to recall which of the stores he purchased the item from).
The ketzos (siman 300) explains that there is less of a responsibility by pikadon because wherever it is, it is considered to be in the reshus of the owner. The nifkad isn't responsible in a chiyuv "hashava", he is just responsible for any negligence on his part. Therefore, when they gave it to him in a way that he wasn't negligent, he is not required to return it. But, one who owes money for a purchase on the other hand, it is like a debt that he owes, and therefore it is his responsibility to make sure that he fulfills his mitzvah of "hashava" even if he wasn't at all negligent.
The Ketzos (222) makes a different distinction based on the language of the Shulchan Aruch/Rambam - ואם הוא חסיד נותן דמים לכל אחד ואחד כדי לצאת ידי שמים
The type of yotzei yidei shamayim being spoken about by the case of the sale is not for everyone, it is only for one who considers himself a chassid. However, normal people wouldn't be obligated even to be yotzei yidei shamayim. Therefore, in siman 300 where we are speaking about the obligation of regular people, the shulchan aruch writes that one isn't required even to be yotzei yidei shamayim.