If you are filling the crates via either the Init.sqs or a script run from the init.sqs, place a 1 second wait period before you load these crates.
Reason is, sometimes if there are a lot of units / objects placed on the map in the mission editor, it can be some time before the engine loads all these units into memory from the mission.sqm and in some cases the init.sqs and other scripts can run commands on something that isnt seen as being there yet