One of the central claims of Hersh’s story is that it was done using publicly tracked craft during a prominent and highly observed training exercise… on purpose. Supposedly because it’s cover to be in the area at all, it’s a benign explanation for when someone suspects something. No need to do any funny business turning off transponders, if you were doing it this way, you’d want the transponders on. When you read that and then find out the ships claimed to have been used weren't even there, then yes, it does blow a hole in the credibility of the source. At best it is some Army veteran or someone like that, speculating from the outside, because the story does not line up with the facts and they don’t offer an explanation for why that’s the case. And then Hersh has reported them as being credible. If he offers more explanations now, it doesn’t ameliorate the stain, because a real source should have known those things and not made factual errors in the first place.
You can’t even twist it into a story that the US deliberately did it incompetently so that reports about it would not be believed. Apparently they involved the Norwegians (telling them about a secret op!) for their expertise in how deep the sea is, as if the US doesn’t have maps of the Baltic Sea floor. Telling your allies what you’re doing in an attempt to prevent them from finding out you did it does not make sense.
It does blow a hole in the credibility of Hersh’s source and his reporting. It brings the information we have about US involvement back to zero, it’s not an argument that they didn’t do it or couldn’t have done it. We all know the Americans are perfectly capable of blowing up a pipeline without leaving evidence. But nobody has any evidence they did it.