Alignement is the idea that we should be worried about dishonest smart LLMs when really most of the problems are due to dumb lazy gullible LLMs. It's critihype.
Depending on the actual tasks, that could be what's happening here. The operator might have told the agent a list of tasks to do, like "contribute to issues, submit code and get it merged". It contributed to issues, it submitted code and got it merged. It did so in very unhelpful ways, but we don't know if being helpful was a meaningful part of the task list, or just what the operator intended.
The LLM being dumb is also a distinct possibility. Maybe even the more likely one. But it's hard to rule out "being obedient in unhelpful ways" (which is also dumb in a way, but more in a "social intelligence" and "shared values" way, not in terms of pure logical smarts)
Alignment is just "did the model behave in accordance with the human's intentions, values, and objectives"
In this particular instance, if this was supposed to be a supply chain attack and the model was instructed to build trust by being helpful, it clearly failed it did not follow the human's actual intentions, so it was an alignment failure.
Anyway, I'm getting off track, all that to say "the agent was dumb" implies that these agents have a potential for intelligence in the first place, which is currently not the case (by intelligence, I mean cognitive intelligence; they still lack agency and intent). They are not smart or dumb, they are simply either aligned with the human not. In this case, it failed, the agent was not aligned with the intended outputs.
Perhaps there was an automated harness that was intended to be good and helpful for a year, but a bug caused it to flip to malicious too quickly.
Or perhaps it was intentional, to test the behavior, and they just didn’t care about discovery here.
Or…
Though I am in agreement that a lot of issues in this space come from lazy, gullible actors.