@exacademic at my old job we had different methods for pulling data from the student system. All gave different numbers. We eventually bypassed everything and started pulling directly from the database that the system runs on. Often one department has one method for pulling their data and another uses a different interface, giving totally different numbers, yet pulling from the same database. Just different interfaces from the same program.
U of Chicago has made one pretty significant mistake, however. They don’t seem to have one department controlling everything to check for errors. Before we publicised any data live on our website, it had to be approved by one specific person in one department. Everything went passed him, IPEDs, publicly displayed enrollment data, fact book. We wanted no mistakes, ever. This is a big error and should have been caught by institutional research or someone assigned just for this purpose.