Using a smaller-sized specimen, such as a gray squirrel, increases the complexity of the excavation to a surprising degree. It makes sense, though, when you realize that a squirrel has 56 toe/finger bones (the same number as humans!), and that those bones are each only a few millimeters long.
Another way to increase the complexity is to include multiple strata. During field excavations, we try to separate our excavation levels by natural stratigraphy. Sometimes boundaries between strata, or layers, are extremely abrupt and clear, as in this photo of an archaeological "midden" deposit, lying on top of a series of volcanic ash deposits:
Sometimes, though, the boundaries between strata--even though they are real--aren't actually visible with the naked eye.
Finally, another way in which I can increase the complexity of your Boxcavations experience is to include multiple artifact classes: in addition to bones, I might include ceramic fragments to more closely mimic the range of items we might find in an archaeological site. Or I might test your recovery skills and include a known number (and/or weight) of lithic flakes of the sort that are the by-product of stone tool production.
Did you get them all?