The above quote from your post explains the cause of your wife's problem. If the departure stamp from Thailand is in her old Thai passport, she should have shown that old Thai passport together with her new Thai passport on her arrival in Thailand.
Now that her immigration record has been flagged with a note that she entered Thailand with her Canadian passport, ie that she used her other, non-Thai nationality in Thailand, she is indeed at a potential risk of losing her Thai nationality. I don't know enough about this subject but I recently saw another website, forgot its name, where they seem to have experts for such questions.