The study focuses on some methodological problems associated with the research of cave sites. A large amount of anthracological material came from the context of the layers with archaeological material from the Pod hradem Cave (Moravian Karst, Czech Republic). Some samples were determined as Taxus, which in this context would be among the first evidence of yew in the Middle Pleistocene. However, their dating showed significant secondary redepositions. Similar redepositions of material were repeatedly found in the dating of material from the Kůlna Cave (Moravian Karst, Czech Republic). Here, too, in certain parts of the cave, there was secondary redeposited archaeological material in seemingly intact sediments. Both caves were inhabited – Kůlna Cave from MIS 8 to MIS 2, Pod hradem Cave – from MIS 3e to MIS 2. At the same time, intensive post-sedimentation processes took place in both caves, accompanied by the activities of large carnivores inhabiting these caves alternately with humans. The last important factor influencing stratigraphy was the archaeological excavations at the end of the 19th and the beginning of the 20th century.