What are some ways rocks can change which might make stratigraphy less reliable

Essentially there should be no differences in how sediments, soils, or older paleontological deposits are recorded. Especially in the case of recent deposits, geomorphology and soil sciences are crucial to appropriate characterizations of sediment or soil formation and development of inferences about archaeological site formation. Unfortunately, a number of conventions used in much archaeological research (at least in the US, and especially in CRM archaeology ) are minimally informed by standard soil development knowledge and process geomorphology. 

This scenario is called diffusion. particles are moving from regions of high concentration to low concentration.