Hi Dino,
Multiple reference inputs with different phases or multiple reference input frequencies at the PLL1 PFD will create some close in spurious. The first image shows a typical setup with a single reference input and wideband integrated jitter (100Hz-30MHz).
Adding multiple inputs which are not synchronous and are different frequencies can yield the result below. This specific configuration uses PFD rates of 20MHz, 25MHz and 15.625MHz simultaneously. It is possible to minimize and even eliminate this noise by powering down the unused input receiver.
The final image shows the same setup with the spurious content included in the jitter calculation.
Please let me know if you have any further questions or if I can help clear anything up.
Regards,
Kyle