Our customer is using TUSB8041 to work with Novatek SoC and added 100nF AC coupling capacitors on USB_SSRX_UP pins for TUSB8041, but they found that sometimes it will cause USB3.0 communication ...

My thoughts were to AC couple the output as that is what is suggested by the downstream component, but DC couple the inputs. This is sensible, AC coupling the inputs in your design will protect ...