a lot of soil mixes come with mycorrhiza... and other microbes to boot. check soil... does it contain beneficials or not?
so, it's a total guess if it is bad or good or irrelevant. overwatering and other info you may have could help...
even if you transplanted, removed some lower substrate, it doesn't guarantee it is gone... one spore could regrow the whole thing. Could spray a litttle fungicide down there, but with a young plant, i'd choose something very mild. e.g. i don't think a copper soap (copper fungicide) would be a good idea.
Clean it up as best you can without damaging roots, and air it out better. e.g. don't have it sitting in water between irrigations... but i'd wait for confirmation it's a bad microbe before anything drastic.