The Apple II's disk system, being largely software driven, lets a sufficiently evil person do all sorts of hideous things to make a disk hard to copy. Apple II drives, for instance, are capable of writing "half tracks" (and even under certain circumstances, "quarter tracks") because the stepper motors are directly controlled and it takes multiple pulses to move the heads to the "official" non-overlapping positions. Likewise, since bytes to be written to the disk are encoded in software an author that really wants to make their disk inscrutable could use a different GCR translation table (or, indeed, just use FM encoding). The creators of copy-protected software would essentially implement their own DOSes to handle whatever bizzare format they cooked up, leaving only a few sectors at the start of the disk readable by normal means. For an example of what was possible with the Disk ][ hardware see the "Spiradisc" format used by Sierra On-Line

Anyway, these sorts of disks do a great job resisting the efforts of simple sector-by-sector copy programs. Your choices were basically:

1: Figure out (via reverse engineering a RAM dump of the disk code) the ugly details of the format and write a *specific* program to copy it, or

2: "Crack" the program by capturing it from RAM and patching it into a normal executable format loadable from DOS. This is what most hackers ended up doing in the end. Which is a good thing because those bizarre disk formats weren't particularly emulator friendly either.