Incompatible software with newer operating system versions
What causes some applications to be pre-identified as incompatible
  while other simply fail to work?


It all depends.  Some binaries are compiled with a flag that indicates which is the minimum OS version it will run on.  There's also the Info.plist that contains minimum OS versions.  Finally, the application itself can check to see if it will run on a particular OS version.

Unfortunately, older apps like OmniGraffe 4 which was released back in 2005 probably don't use any of the version checking (and is incompatible) which is why it crashes when launched.