Are you talking about Outstanding Reconciliation items on the monthly report? We would occasionally have batches reported as missing, typically when the Sunday was at the very end of the month, and might not have been processed by the bank until the first of the next month. After checking with the record in MLS I would confirm that they were indeed deposited and they would be resolved by the next months statement. I am still amused when I get a notice that MLS has recieved record of a deposit of $XXXX, but the bank has no record. and at the same time recieve a notice that the bank has recieved a deposit of $XXXX (same amount) but MLS has no record of it. I haven't worried too much about these as they have always resolved themselves.
A few years ago CHQ informed us that our bank was missing a deposit of $!0,XXX and at the same time notifying the other ward in our building, who uses the same bank, that they had an extra deposit of $10,XXX. I guess these things are just generated by computer or something, because it seems a human would see this and immediately put these two things together.