The autoregressive engine should see whenever the model starts emitting tokens under the user prompt section. In fact it should have stopped before that and waited for new input. If a harness passes assistant output as user message into the conversation prompt, it's not surprising that the model would get confused. But that would be a harness bug, or, if there is no way around it, a limitation of modern prompt formats that only account for one assistant and one user in a conversation. Still, it's very bad practice to put anything as user message that did not actually come from the user. I've seen this in many apps across companies and it always causes these problems.