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@JonoMarshall
The only way I can imagine an auto-embed happening is if you drag an image file to the illustrator icon or open it using File -> Open, this then assumes you are editing an image file and will save-down (or whatever) once the edit is complete... in this way the illustrator file can match colour options of the document to the image that is being opened (meaning your workflow isn't unintuitive).
If pulling an image into an existing/created ai file (whether saved or not) you should never get an auto-embed happening (as far as I'm aware) as there would be a colour space conflict that cannot be resolved without the application making an assumption (potentially ruining your workflow).
You can embed as needed easily enough using the links palette or the large "embed" button with an image selected... I'd avoid this though?
Sorry that's all the thoughts I've got, I vote it was a glitch?!