Yes, this was the case with Gemini 3.0 Pro Preview's CoT which was in a subtle "bird language". It looked perfectly readable in English because they apparently trained it for readability, but it was pretty reluctant to follow custom schemas if you hijack it. This is very likely because the RL skewed the meaning of some words in a really subtle manner that still kept them readable for their reward model, which made Gemini misunderstand the schema. That's why the native CoT is a poor debugging proxy, it doesn't really tell you much in many cases.

Gemini 2.5 and 3.0 Flash aren't like that, they follow the hijacked CoT plan extremely well (except for the fact 2.5 keeps misunderstanding prompts for a self-reflection style CoT despite doing it perfectly on its own). I haven't experimented with 3.1 yet.