I work in IT for a bank and agree that account reconciliation is complex. However once you have it set up and all the connected financial institutions pretty much share the same ways to do it then in the absence of "impacting events" (network outages etc.) then everything rolls on in an automated way. With hundreds of millions of transactions per month per acquiring bank there is no other option.

I'm on a team which investigates "why something went wrong" at an individual level. For example you buy something but get charged twice, whatever. There is not that much volume of these and we're not a large team.