Well, the most common problems would probably be An upper respiratory infection (U.R.I. or R.I.), which is most commonly bacterial, but can be viral. If you catch it quickly, you can cure it by raising the temps a bit, making sure the cage is not wet, and removing most of the substrate to make the cage basically "sterile". If it has advanced the best bet is to get to an experienced reptile vet and get cultures done to determine the exact cause of the R.I. and get the appropriate antibiotics if necessary. Many inexperienced vets will just randomly prescribe baytril, which has a range of side effects, and may or may not be effective depending on the strain of bacteria. I have found Fortaz to be a bit more effective, and less harmful, as a general antibiotic.
Then there is stomatitis (mouth rot), and scale rot. These can be easily cured with home medications if caught early. a chlorohexidine solution (like nolvasan) or a 50/50 mix of hydrogen peroxide and water, used as a mouth rinse can clean up stomatitis. Scale rot can be cleaned with peroxide, then betadine (or any povidone iodine solution), and a touch of neosporin. If they are advanced you may need to get antibiotics. Most of these problems can be easily avoided, and are generally the fault of the keeper and improper husbandry, as are the reasons for an R.I. A wet, dirty, &/or moldy cage and substrate is the general cause of scale rot. And stomatitis is generally from a mouth injury, from feeding live prey on a loose substrate and the animals getting a wood chip or something caught in the mouth.
There are a whole load of parasite problems. Worms of various types. This is mostly a problem with wild caught imports in snakes, And some lizards that have to eat live insects. Panacur is the easiest solution for these, and is fairly safe, readily available, and easy to do yourself. Of course you need to be able to do a fecal test to confirm the problem. Then there are intestinal flagellates, & protozoans, which are normally treated with flagyl. And there is coccidia, which is common in all insectivores. It actually probably exists in all of them all the time, but if the load gets to heavy, it can lead to digestive problems and dehydration among other things. The best thing I have found to treat this is albon. If I treat an animal with any of the above I always use a probiotic afterwords, something like acidophilz+, it is the equivalent to a person eating yogurt, to restore the beneficial gut flora, as allot of that is destroyed along with the bacteria and worms you want to destroy. Especially with the albon and flagyl.
Then there are the more complicated problems, Like Inclusion Body Disease, (IBD). Nobody is 100% sure what exactly causes this, or even how it is transmitted. All pythons and boas are susceptible, it is very contagious, and it is fatal. If you read the most recent research on it, it sounds like the original research on aids back in the 80's. There is the search for the mysterious retrovirus that scientists think is causing it, but has yet to be found. So there is not a 100% test to even see if an animal has it, the only way to confirm is a necropsy, to look for inclusions in cells in the organs.
Then there is cryptosporidiosis, commonly called crypto. This is not fully understood yet either in my opinion. There is a thought that most reptiles have it, are asymptomatic carriers, and stress can lead to increased loads, which can harm and kill the animal. And there is a school of thought that though there may be SOME asymptomatic carriers, if an animal is infected with it the prognosis is grim. I don't have enough experience with it to have an opinion as of yet, and have kept animals for 25 years, go to 2 - 8 shows a year, etc.. Which means it can't be THAT common, in my opinion. Or maybe all of mine have a normal load, are generally healthy, and good hygiene and sanitation practices keep it in check, similar to the coccidia found in most lizards. So maybe a toxic cryptosporidiosis infection isn't that common, but the cryptosporidiosis itself is. This is actually my best half educated guess. Of course, I may just be lucky.
And then there is the ubiquitous snake mite,
Ophionyssus natricis. This is probably the most likely common problem with anyone with a group of reptiles. If you think getting rid fleas in a carpeted house with cats and/or dogs can be tough, or was before all of the current medications available, this can be much worse if you get an infestation in a group of reptiles, which can happen very, very quickly. It is actually easy to avoid with simple precautions, and fairly easy to treat if caught early, and you are THOROUGH. You do have to attack like an act of war though. Leave one small piece of moss or branch in a cage, or on the floor in another room, and a week later, your back to square one. There are homeopathic and green remedies on the market now, but for my dollar a product containing permethrin, used safely and properly is the way to go. There are products for reptile on the shelves now that use permethrin, the most common is
Provent a Mite. But that stuff is pricey. There are products with the same ingredient elsewhere and cheaper. Nix, for example, if diluted properly, is great for treating animals and enclosures. And rid makes an aerosol spray, "Home Lice Control Spray for Surfaces", which is great for areas around the enclosure, walls, carpeting, etc... Be careful of the rest of the rid products though, the shampoos and creams contain Piperonyl butoxide &/or pyrethrum which can be harmful or fatal to reptiles.
There are various other things that can happen, injuries from rodent attacks for those who feed live, and insect bites, especially from the newer
Jamaican Field Cricket, Gryllus assimilis, plus just good old fashioned accidents, bad sheds, refusal to feed, etc... Most minor injuries can be treated with betadine (povidone iodine) and neosporin, or their generic equivalents.
Most of these things can be prevented with proper husbandry, hygiene and sanitation, and good quarantine procedures with new animals.
Wow, I wasn't planning on writing a novella. My mother told me I should be a vet when I grew up...