Tool/software:
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Just to confirm, you are using the 4-lane SERDES, right?
You can use an internal ref clk for SGMII (or USB3.0) but not for both interfaces simultaneously, as the USB requires SSC (spread spectrum clocking) and SGMII does not support SSC. you will have to use external ref clk for the other interface.
In case you want to use 2-L SERDES for SGMII and 4- Lane SERDES for USB, then you could use the internal ref clk option for both.