The linear blend skinning node only supports dense 4 bones per vertex and is not compatible with blend shapes or motion vectors. The meshes that show issues use 2 dense influences per vertex. Use the compute deformation node if you want to keep 2 dense influences per vertex. The limitations can be found in the documentation: https://docs.unity3d.com/Packages/com.unity.entities.graphics@1.3/manual/mesh_deformations.html
Lastly, a kind reminder that mesh deformations in Entities Graphics is experimental, features are missing.