I worked with teams integrating legacy systems from hospitals before. There seem to be a large amount of carefully customised scripts for pulling data together.

I worked with teams integrating legacy systems from hospitals before. There seem to be a large amount of carefully customised scripts for pulling data together. There was never a straight-forward data ETL / export for something other than routinely reported. A lot of information is derived and inferred from even not related (e.g infer chemo events from drug prescription codes if parts of system is not accessible). Hence if you really need high quality data you need a lot of validation and cross-checks as well (either by script or manually). To me it sounds like the checks and validation did not happen enough as the time is very critical. I don't think Excel is the single thing to blame here. Hospital IT systems have a long history of data related issues.