Neither of the examples you are providing are ideal approaches, but personally I might prefer the first one. It kind of sounds like they are asking a question but badly. But it is possible to approach this kind of conversation way more tactfully. And to the advantage of the manager because people will be more comfortable and less defensive.

There are a million ways your scenario could happen. Another possibility is that the manager misunderstood something. My last boss was notorious for approaching people, very serious and grimly, with accusations of wrong doing. then when the worker would go ask the “accusor” it would turn out to have been some totally innocuous comment or like someone making a joke or mild social-type complaint or giving feedback on the workplace as a whole. And this included situations where multiple people were present and everyone agreed, so its not just someone lying to preserve the relationship. I was on both sides if the exchange myself. When i heard that i had made an “accusation” I had made I really had to think hard to figure out the grain of reality it was based upon. That’s just one example of what could have transpired.

As you may infer from that story, “accusations” were pretty commonplace. And it was overall a good job, just that manager didn’t know how to do their role. 2 in 4 years is a pretty good run.