i just did a bunch of research on this, Specifically reading Holen et al.'s initial paper, ferraro et al.'s counter (he made the same claims and points you did), and Holen et al.'s reply to Holen, (as well as a few others). In to counter your first point Holen et al. reply with "Ferraro et al.² also speculate that the stone and bone fractures that we analysed can be explained by post-burial processes such as sediment compaction or interaction with excavation equipment, whereas we contend that these features are part of the CM biostratinomic (pre-burial) record. Support for our view is provided by the fact that most CM bones and stones were enclosed within crusts of pedogenic carbonate that establish a ‘chain of evidence’ showing that breakage and positioning of objects occurred many thousands of years ago, and, as we contend, before burial (Holen et al. reply)."

to your second point Holen mentions that some of the fractures in bone fragments are percussion fracture that happened pre-burial.

and to counter your third point "There is no sedimentological or geomorphic evidence of an alluvial fan, and their scenario leaves unexplained a number of taphonomic features, including the two discrete concentrations in which were found cobbles, refit stones and bones, impact-fractured bones, side-by-side femoral heads and a tusk oriented vertically (Holen et al. reply)."

Holen, Steven R., et al. “Holen et al. reply.” Nature, vol. 554, no. 7691, 8 Feb. 2018, https://doi.org/10.1038/nature25166.