I think this is an important distinction and the answer is that it is hard to distinguish. People often bring up the
Simple Sabotage Field Manual in situations like these and I think there's something that is often missed: the reason the techniques in here are effective is because they are difficult to differentiate from normal behavior. This creates plausible deniability for the saboteur. Acting too hastily could mean losing someone valuable for a genuine mistake. I'm saying I agree with the Amazon example. (You can also use saboteurs to your advantage if you recognize that they are hunting down and exploiting inefficiencies, but that's a whole other conversation)
But my understanding of this case is that the actions do not appear like simple easy to make mistakes. As I understand, the claim was that the intern was modifying the weights of checkpoints for other peoples' training results in an effort to make their own work better. Mucking about in a checkpoint is not a very common thing to do, so should make someone suspicious in the first place. On top of this it appears he was exploiting weaknesses and injecting code to mess with peoples' optimizers, and to do things that do not have a reasonable explanation for.
So as far as I can tell, not only was he touching files he shouldn't have been touching (and yes, shouldn't have had access to), he was taking steps to bypass the blocks there were in place and was messing with them in ways that are very difficult to explain away with "I thought this might be a good idea." (Things that explicitly look like a bad idea). If that is what in fact happened, I think it is not a reach to claim intentional sabotage. Because if it wasn't, then the actions are represent such a level of incompetence that they are a huge liability to anyone within reach.
[0] https://www.cia.gov/static/5c875f3ec660e092cf893f60b4a288df/...