That is strange. These are fairly obvious things, but do you have a filter in there that could be sucking them up? Or could you have accidentally siphoned some up during water changes without realising? I'm no expert but I can't see them cannibalising since they filter feed tiny particles from the water.
I don't know anything about methylene blue but I wouldn't have added any kind of chemicals (if that's what it is? I have no idea). I would have thought that the fungus would be a good thing because it helps you to easily identify which eggs are unhealthy/unfertilised and need removing.





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