My design uses the compute module 3+ board from the raspberry pi foundation. I used the FSUSB42MUX schematic from the CMIO board to have a slave/host USB port. My problem is the D+ and D- lines are not being pulled up to 3.3 V, they have been pulled up to 5 V. I am attaching both the PCB and schematic design incase anyone can see any easily visible issues that I can not. HDMI output is working fine, as well as the SD card lines. All USB traces have been routed as 90 Ohm differential pairs.
Please let me know if more information is required.