I've fed my eldest on cocobark, eco earth and shredded paper over the years. He's also my fussiest one where he will usually refuse FT and just eat live.
Never had a problem. He's over 20 now. My current batch of noodles are all on ecoearth/cocobark. No problems there either.
EcoEarth is so fine that you shouldn't have a problem if they eat a little bit. Yes, it cannot be digested, but it's not a lot of it with how often they eat and all. If you have them on repti-bark or the larger wood chips and they swallow a larger chunk then that could potentially be an issue, so just make sure to use the smaller wood chips.
It sounds like a wood mite or if he'd fed live, it could have been a rodent mite. Reptile mites are small black little ones by the time they're able to be seen with the human eye.
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