I've experienced this in "some" events and it is constantly the same grouping of players, who attend one regional final that we experience problems with, it is mostly the chip race that we experience that when they return someone somewhere will claim that they had x instead of what they now have, we could do little about it, auditing the entire tournament to count the stacks did not prevail anything, and often would result in a wildly inaccurate in play count, we simply had to come up with a figure that everyone at the table agreed upon and give it to them. In other events with players from different regions it was much easier, it has happened twice from memory, and the chips had gone to the player who was 'buying' the redundant chips, therefore no need was ever made for additional chips to go into circulation.
We have since clamped down severely on the region that complains practically each regional final they have, we supervise the emptying of the cardroom more strictly, and ensure we have a totally sterile cardroom, when racing off one floor races the table and the TD or Manager will remove the chips from each table, colouring up what he has removed as he goes. The end result was the last two events we have held for that region have not had any issues when returning from breaks.
We have had situations like your previously, namely (same regional final players again) someone stole the high denominations from a stack of sets which were already out on a table, to be frank there is little to nothing you can do, unless a camera catches it (this was in a casino but unfortunately the cameras surrounding the table did not catch the culprit!)
Unless you can get some consensus at the table as to what has happened to return the chips to the player from another players stack, you just have to issue additional chips into play which I detest doing, as effectively you are aiding and abetting illicit conduct at your tournament.
Tightening up on your security measures is the only way to try to prevent issues from occurring.
Regards
Stuart