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I asked this question which says it has 3 replies but it only has a single reply by the automoderator.
If you have to ask if something bad concerning Reddit is caused by Reddit admins, at this point the answer will always be "yes."
On reddit you'll see reply counts reflecting replies of any user, including shadowbanned ones. You won't see shadowbanned comments though. That's why you see 3 count but not the comments. Chances are those comments are from bots who were shadowbanned.