yes it can tell. thats where your o2's come in. once it has seen a consistant mis, it looks at those o2's and can see that there is way to much fuel there.
now i will correct myself on one part. it is possible to have a staedy mis, with the cel flashing and it be fuel related. a leaking inj would do that. but the fdm, eh, i think if the fdm was going out, the car would just run like poo all around. missing from every cylinder. and probably would be very hard to get to go anywhere if it were to go at all.
Misfire type A:
Upon detection of a Misfire type A (200 revolutions) which would cause catalyst damage, the MIL will blink once per second during the actual misfire, and a DTC will be stored.
Misfire type B:
Upon detection of a Misfire type B (1000 revolutions) which will exceed the emissions threshold or cause a vehicle to fail an inspection and maintenance tailpipe emissions test, the MIL will illuminate and a DTC will be stored.
thats from ford......so the only thing that will damage the cat for this to happen is.....FUEL