Other than drivers for early hard disks like the HyperDrive or Corvus which used their own schemes for partitioning, like "drawers", there wasn't much that didn't work. I can't remember anything else that broke. I retired my 1-year old $2000 10MB Corvus in favor of a SCSI MICAHDrive which was 20 times as fast. General Computer issued HFS-compatible software, as I recall.

HFS very cleverly kept almost complete compatibility with MFS by making a folder (subdirectory) look exactly like the structure of an MFS disk. Apps like my MacMovies written to "bare metal" in assembler work in the Plus like champs. Toolbox calls were the same, though new ones were added in the 128K ROM. The very earliest demos like Pepsi Caps and the early version of Alice that doesn't support the Finder run on a Plus the same as they do on a 64K ROM. There may be incompatibilities, but I don't know of any. There certainly wasn't "alot".