The critical thing is that the Load Plan and the Loadsheet agree, and are cross-checked by the Despatcher (or "turnround co-ordinator"), the load plan having been signed off by the loaders, before the aircraft is allowed to go anywhere.
Whilst the Centralised Load Control hub may of course be at fault in cases, the technology is such that it is not generally possible to produce a loadsheet which differs from the loading instructions, or a loadsheet which is illegal (out of trim / overweight).
Therefore in most cases of loading errors, it is down to communication or human error.......
a) version 1 of a Loading Instructions being used when there has been cause to re-issue a version 2.
b) Loaders getting their holds mixed up....."all in the back" becomes "all in the front" for no apparent reason (yes, I have seen that happen!)
In many cases, interaction from the crew trying to impose a "standard loading" can be dangerous as it presents the ground staff with a conflict. However, it is not uncommon for this to happen......particularly from flight deck of charter carriers who tend to have a simpler loading pattern, and are also (at many stations) closer to the load control area in that they have to do manual loadsheets. This tends to be less true of most scheduled carriers where the loading pattern tends to be more varied (2 class cabin, freight carriage, etc.), and the crews are used to leaving this activity to the groundstaff, plus there is generally no 'standard' anyway.
If the computer and all paperwork is based on a particular load distribution and a Captain asks for something different, then straight away there is the potential for a trim (and legal) discrepancy. The computer system and data would have been approved by the airline's weight and balance department (as per the IATA AHM560 process) and therefore the critical thing is ensuring all the cross-checks on the ground are in place such that the aircraft is loaded as per the sheet of paper the Despatcher delivers to the pointy-end!!
In trim.