Users can be very creative sometimes 😉
But the screenshot does rule out input from Excel as this would be shown in the audit.
What is not shown in the audit is if a rule clears / overrides the data. You are saying that only some of the data is cleared in the form and not all data in the affected data unit? If so, that seems to rule out a clear data DM step as well - leaving only rules.
My strong guess is that there is a rule somewhere in the system that pushes no data on to those affected cells. Now to the fun part, to pin down when that happens exactly (every time a consolidation is run? After a custom calc? A DM step? ...?). As this seems entity specific, maybe there is a special rule run only on that entity, or only that entity enters data in the intersections which would explain why other entities do not experience the same.