Help with very small hold time violations

Is clock path pessimism removal enabled? You would see a line item in the Path Summary tab. The clock tree uses a slightly faster sub-model to the source register and a slightly slower sub-model to the destination register, which models On Die Variation. Of course, when it's one clock feeding the same register, there is no On-Die Variation. The Common Clock Path Pessimism Removal is what adds back delay to counter this pessimism. If it's not on, you can turn it on under Assignments -> Settings -> TimeQuest.

Note that it's impossible to have a hold failure where the same clock is the source and destination, since the data delay will always be positive, and the clock skew is exactly 0, since it's only a single edge in question.

Also note that I have seen failures like this in some older versions of Quartus with early timing models, so make sure you're up to date.