STM32F769 USB FS Pin PB13 Question
The note in the datasheet should concern you if you have VBUS detection enabled. PA9 and PB13 are used for that and thus they can't be connected to other peripherals in such case.

If you don't need to sense USB VBUS, just disable that feature. It can be done by clearing the appropriate bit in the OTG_GCCFG register (check the Reference Manual page 1587), although possibly they may are easier higher level ways if you are using standard or HAL libraries. If you say Cube MX didn't complain, probably it didn't enable it as it's disabled by default, but you can't never know with Cube MX, better check.

In short, make sure that VBUS sensing is disabled and you're good.