There are some other failure modes that all feel kinda vaguely related that probably help with building a hypothesis about what's going wrong:

Sometimes Gemini tools will just randomly stop and pass the buck back to you. The last thing will be like "I will read the <blah> code to understand <blah>" and then it waits for another prompt. So I just type "continue" and it starts work again.

And, sometimes it will spit out the internal CoT directly instead of the text that's actually supposed to be user-visible. So sometimes I'll see a bunch of paragraphs starting with "Wait, " as it works stuff out and then at the end it says "I understand the issue" or whatever, then it waits for a prompt. I type "summarise" and it gives me the bit I actually wanted.

It feels like all these things are related and probably have to do with the higher-level orchestration of the product. Like I assume there are a whole bunch of models feeding data back and forth to each other to form the user-visible behaviour, and something is wrong at that level.

At one point it started spitting out its CoT in the comments of the code it’s supposed to be changing.

Ah yeah I've seen that too. Definitely seems related.

I suspect this is also something like the "inverse" of a prompt hijacking situation. Basically it's losing track of where its output is flowing to (whereas prompt injection is when it loses track of where its input is flowing from).