I opened an issue on the main repo first (langchain-ai/langchain#29515) since I wasn't aware the experimental utilities had their own repo.

I won't bother reproducing the text of the issue but my problem boiled down to this line:

The default "method" parameter is "json_schema" for ChatOpenAI and this results in success. However, for ChatOllama, it is "function_calling" which results in the parsing errors mentioned in the issue.

To get ChatOllama working with constrained nodes, I needed to change the indicated line to:

structured_llm = llm.with_structured_output(
    schema, method="json_schema", include_raw=True
)

I'm not sure what the general correct fix is. Perhaps the method should be passed into the LLMGraphTransformer constructor?