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"But if, as it appears, the problem is a previously unrecognized limit on the number of files that can be stored in the craft's flash memory, then Opportunity's data collection and file management can be planned to prevent the problem."

It sounds like more of a problem in the flash memory's file limitation. It could be as simple as the programmer not reading the specs on the memory, or the memory manufacturer may have mis-published the spec, or it may be an undocumented feature(bug) in the memory that the manufacturer was unaware of.

So far they have handled this very well IMO. Mariner 1 was blown up at launch by the range safety officer when it flew off course at launch because of a misplayed comma in the guidance coding.