According to an interview with Famitsu and confirmed by Silconrea, there’s a hidden secret inside NieR: Automata that players still haven’t located. Below is one one of the highlights from the piece that was pointed out, signaling that there’s something still hidden in the game that players have yet to discover and that when they do it will be “bad’.
“That” has yet to be found. Since the developers feel that it would definitely be bad, they have yet to make it public. Due to various circumstances, this something made its way into the game. Since they feel that going into any further detail might cause some problems, they won’t say more about it. Think of it as NieR: Automata’s last secret.
What exactly “that” is, good luck even getting a hit for as there’s no indication of what it could be, as it could be anything from a hidden item all the way to a secret ending. One thing is for certain, though. If you don’t think this won’t trigger hundreds of dataminers to comb over the code and locate it, you’re crazy! Until someone locates it and tells us what it is, there’s no telling what this could be or how it could affect the game.