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.
I absolutely love running and now have a new appreciation for my Achilles Tendon.This is a useful skill, allowing us to escape from predators, catch prey, win medals, and so forth. We’re now so good at it that some hunter-gatherers use their endurance to chase after animals for hours until their prey collapses from exhaustion and can be easily killed (Bramble and Lieberman, 2004).
cliffelam made this point in the #tngpodcast on running when he said, "Running is all in your head, your legs are perfectly capable to take you anywhere you want to go. I mean, we are genetically designed to run down any animal that has ever existed on the planet".
I'm always a bit wary when talking about endurance running, particularly in the context of the Bramble and Lieberman study. Whilst they do make some valid points about the importance of endurance running amongst some modern tribes; they then go on to claim that a large part of modern anatomy evolved to enable endurance running. That second part is almost certainly wrong. Many adaptations appear to benefit long distance carrying and walking more than long distance running; and persistence hunting as a strategy is more energy intensive than persistence walking (which is why few modern groups practice it, but many more engage in persistence walking). That's not to say persistence running isn't important to those groups which now do it, nor that it had no influence on our evolution; it's just the endurance running hypothesis overstates this importance and I fear lending credibility to it.