I read of a case where the MSer deposited via ATM and several weeks later the bank clawed back the amount saying the envelopes were empty! The MSer didn't keep his/her stubs and had to "eat the loss" since they've thrown away all receipts. Best to save MO receipts/stubs/bank receipts in situations like this.
I prefer depositing via app, scan using desktop or deposit with teller while also keeping stubs of MOs I deposit and staple them with receipts that I can easily retrieve in case of bank discrepancies weeks/months later.