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They're small, so easily disturbed by natural forces, broken/damaged or just missed entirely during excavation. There was a study a few years back in which they sieved through all the mud that had been excavated from an archaeological site and found hundreds of extra bones (most of them of small animals, or the small bones of larger animals such as heel bones). Unfortunately this process is very time consuming - which also makes it expensive - so is not routine practice unless it is believed a deposit is very likely to contain small bones of great importance.