Wild-caught fish are taken from lakes and rivers, transported to holding facilities, held until export, then shipped in bags for anywhere from 24 - 48 hours (sometimes longer). Then they go through a second acclimation at an importer's facility, while potentially coming into contact with pathogens/bacteria/viruses carried by the other hundreds or thousands of fish that have also moved through the facility. They are held for maybe a week or two (if we're lucky -- some people turn around and re-ship them a day or two later), then re-shipped to a customer where the acclimation process starts again. If that customer is a pet store, the fish basically goes through the same exposure and acclimation again. Some fish may be shipped/moved as many as three or four times in as many weeks. That kind of constant stress takes its toll on fish in various ways, but ultimately it wears them down and causes their immune system to falter, leaving them open to disease. It's a lot for fish to handle.
I recently bought 40 wild M. ramirezi and lost six in transit, then another 10 over the course of two days. They came in with some kind of funk which I'm treating with acriflavine. I have seen Uaru fernandezyepezi and Pterophyllum altum come in with velvet. Exporters at the holding facilities in South America will sometimes try a broad-spectrum treatment on the fish before they are shipped out, but you have no way of knowing whether the treatment was completed successfully, or whether the fish were allowed to recover from the stress of said treatment before being packed up and shipped out. The same can be said of the importers who are buying these fish and reselling them to us. Some of them hold fish for a few weeks and treat prophylatically to clean them up, others just receive them and ship them right back out to customers.
There are other things to consider. A lot of South American fish, particularly blackwater fish, come from very pure, clean water. The extremely low pH inhibits the presence of high loads of bacteria. Once you introduce them into an aquarium environment, they're likely being exposed to higher bacterial/viral loads than they experienced in the wild. Combine that with their compromised immune system brought on by stress, and potentially overcrowded tanks with questionable water quality (high ammonia/nitrite/nitrate/DOC), and it can be too much for the fish to deal with.
The best option is always to find F1 fish, or find a seller who has already gone through the process of acclimating and treating the wild stock. This is tricky, because it's not cost effective for importers and sellers to sit on fish for a month while they treat and acclimate them.
As buyers, we can minimize our chances for issues by preparing ahead of time to receive these fish. Know that when they come to you, they've had a long, stressful journey and will need a month or two to really settle in and acclimate to your tank. Every time I buy new wilds, they get their own quarantine tank in a quiet room away from the rest of my fish. I leave the lights off for a week or two to let them rest and calm down. They get frequent, large water changes to reduce viral/bacterial/DOC loads, a mix of good quality frozen, freeze-dried, and prepared foods to beef them back up, and a three-stage treatment for intestinal flagellates/parasites, flatworms, and roundworms/nematodes. I also treat for externals if the fish show signs of them. This is a long, slow process because most treatments last 7 - 10 days, then the fish get a week or so break between each treatment. It takes me about two months. When we think of quarantine, we usually think of keeping our current stock safe from anything brought in by newcomers, but it also works the other way too.
That level of quarantine may sound exhaustive, and like overkill, but I rarely lose wild fish when acclimated this way. I've bought almost exclusively wild cichlids for the past six years and other than DOA, I have rarely lost a single fish. The rams I mentioned before are a different story, but I think that has a lot to do with the fact that they were re-shipped to me only a few days after import and their bag water was freezing cold when they got here. It was just too much stress on their little bodies.
My advice to anyone buying fish, but especially wilds, is to know the species that's coming and plan accordingly. Be ready to quarantine it properly and care for its specific needs. Don't introduce them to your existing fish until they've had time to settle in and regain some of their strength and health. Being chased around or threatened/dominated by existing tankmates adds yet another level of stress that may push them over the edge. Hit up a Petco $1/gallon sale, get a 40 breeder or 55 for quarantine purposes, a cheap Aqueon Pro heater, and two sponge filters. You don't even need a stand, or you can get a used one for cheap on Craiglist. For $100 or less you can have a quarantine tank. It's a smart investment that could save you hundreds in lost fish in the future.