My guess for these is that the material tags have changed since the mods last update. For instance, The Bastioneers uses a mixinto to mess with the material tags for all of the types of wood. Depending on how mixinto works (I don’t know exactly), it either just adds to the existing tags, or it replaces them with it’s own. If it’s the second option, then (my guess) is that the problem arises from the Bastioneers mixinto for wood does not have the material tag “wood”.
“material_tags”: “stockpile_wood wood resource”
“material_tags”: “stockpile_wood raw_wood resource raw_material”
The same thing is probably happening with clay, if this is the problem.