I'm not sure how to troubleshoot it, I was just running some baking tests on a simple object and I noticed that only the ID map had an issue, I've tried high resolutions, 8x8 subsampling but it doesn't matter.
The left side comes out clean while the right side comes out with artifacts / noise, I don't know what to call it.
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I usually disable diffusion and AA on my ID bakes when testing as it tends to reveal issues more readily that way