Worms
  Pin worms, Tapeworms, Whipworms, these all rarely show signs. If there
 are signs, it's poor flesh condition and growth rate. In whipworms, the feces
 have blood on them. Pin worms will show by having little flecks of white specs in the feces. I use Wazine/Piperazine as a preventative measure against Pin Worms. Diarrhea is also a sign. The use of a wormer and strict
 sanitation is the only way to prevent, cure this. Also keep other animals out of the hutch.

Fly Strike
The flies lay their eggs on anything that's decaying or a cut on a rabbit. The eggs turn to maggots and only in hours begin to feed on the animal and kill it. Cleaning the rabbit pens will prevent fly problems. Also dead babies in nest boxes also attract flies, so check your boxes.
The flies are attracted to any damp area, so try to keep things dry and clean, and the area should be free of weeds. If there's a compost pile, move it far away from the hutch or cover it up with a tarp. Once a rabbit has fly strike, the wounds need to be cleaned and disinfected. Apply antibiotic ointment and keep the rabbit inside. Clean the area he/she was in and check anyone else for fly strike.
 

External Parasites
There are 5 external parasites:
1. "Warbles" have these signs: swelling or an isolated "lump" around the neck and/or shoulders. This shouldn't be confused with an abcess. This is from a Botfly. I would advise to take a rabbit with this to a vet so the parasite can be removed. Keep flies out of the hutch.
2. Loss of hair in a circular pattern is a sign of Ring Worm. It is more common on the feet and legs on young rabbits, and for adults it can be anywhere. It is a fungus that IS contagious to humans. I suggest to cull these animals, but if you want to save it, isolate him from the herd and treat him with iodine on the infected area(s).
3. Fur loss around the face, neck and back are a sign of fur mites. Cat flea powder can be used to kill them.
4. Mange Mite Infestation causes the rabbit to scratch itself constantly, and it often leads to head trama from shaking its head. Loss of hair on the chin, head, neck and base of the ears are also present. You're supposed to treat it with 7.5% Chloroform & 0.12% Rotenone or 0.5% Malathion containing dust. I would seek out a vet first.
5. Ear Mites (Ear canker) is infecting the rabbit if its shaking its head, and scratching its ears and has a scabby formation inside the ears. Use oil in the ear for 3 days to kill them. Treat both ears, even if only one is infected.

Coccidiosis
  This is a parasite that attacks the digestive tract. There are 2 forms. The
  first is the Intestinal Form. The signs are Diarrhea, poor weight gain, poor
  flesh and fur condition, and is pot bellied. The second form is the Hepatic
 Form. The signs are Diarrhea, poor flesh and fur condition and large white
 spots on the liver. The treatment for both forms is the use of coccidicide on
     a regular basis. To prevent this, you must use excellent sanitation.

Abnormal Parasite
This is a migration of parasite larva in the central nervous system. There are no signs until the rabbit is paralyzed. There is no treatment, and it's best to but the rabbit down, rather to have it live in a vegetable state. The prevention is controlling urine contamination in the rabbitry.