The 3 output SI5351 has all the output stages running off a single common supply rail which makes it hard to stop any interaction/product mixing of signals and it appears to me that there is something in the layout of the Adafruit pcb that magnifies this problem.
It may just need more on board supply decoupling, I haven't bothered to pursue it to find out.
If you look at the 10 output SI5351 devices, they seperated the supply rails so that only two outputs share a supply rail, making them easier to decouple (i.e. 5 supply rails for the output stages).
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