All carriers will use some form of automated system. The checks and cross checks are pretty extensive but like all systems designed by humans, not infallible if the right set of circumstances line up. That's why the checks and balances are all there in the first place- despite everyone's best efforts, errors will occasionally be made.
I must admit that whilst I'm pretty familiar with the QF load control system, from the description you've provided I have NFI what issue it is you've described- particularly an issue that would cause reversion to a full manual load sheet.