They are most likely mites. Did you notice the color? White or amber colored are probably grain mites and they tend to show up in ff cultures and compete with the ffs for food. They are a nuisance but not too damaging in a vivarium. Red or rust colored mites can be directly harmful to...well, everything. Those need to be eradicated with miticide or other forms of treatment.
Sometimes there's no way to be sure because there are thousands of species and they can be hard to tell apart. My advice is to dump the cultures and start over with untainted stock.
Yes, it's a good idea to separate your cultures from your tank, and even from each other. Some place the cultures on "mite shelf paper", which keeps them from migrating.





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