The latest version of CubeMX (4.21) with F4 Libs (v1.16) using the SDIO controller seems to have broken FatFS support. ff.c needs a file that declares the character sets being used because it contains a couple of utility routines. This may only be needed for long file names but regardless it is missing. I fixed it by copying the ccsbcs.c file from the repository (under Middlewares/Third_Party/FatFs/src/options) and it resolves the issue. This was not a problem in earlier versions.
Also, is the system ever going to support wide bus operation with DMA without the user having to manually configure this?