Basically you nothing to worry about...
Dragon, geckos and skinks get tiny red or orange mites on them in nature. These are parasitic but not pathogenic like the snake mite (=dark brownish through to black, as mentioned). These brightly coloured non-pathogenic mites are often found in the ears, armpits and groin areas of lizards, where the skin is thinner, and around the edge of the eyes. They can also be found in skin folds, where these are present. They are no worse than having a tick on a lizard and consume considerably less fluid. And the odd tick, while they look unsightly, essentially does the animal no harm.
In dry enclosures the larval stages of these parasitic but non-pathogenic mites tend to desiccate and the mite population dies out in a matter of weeks. In a consistently more moist environments, they well may be able to perpetuate themselves.
Getting rid of them is quite easy and does not require use of miticides (such as Ivermectin) which are toxic if an excessive dose is used. You can pull them off with tweezers or simply daub them with a cotton bud soaked in cooking oil. The oil blocks their breathing holes (spiracles) and they suffocate – so it takes a while for them to die. If there are heaps, then you can use the spray-on cooking oil.
You don’t need to dismantle your bioactive enclosure. Assuming they are parasitic mite, simply remove the lizards, treat the mites, then either rehouse the house the lizards until the life cycle is broken or repeat the procedure daily until there are no more mites on the lizards.
It is important to realise that there are also a number of brightly coloured free-living mite species. Given the degree of movement you said you observed, it sound very likely that the mites were a free-living species. What you need to do is check to see if they began to settle in the area of the lizard that I mentioned earlier. If not, this like confirms that they are a free-living species. In which case, you have clearly had a bit of a population explosion. Mother Nature will take care of that soon enough. All part and parcel of having a bioactive environment.
