I recently had a problem in one of our designs that was caused by assigning a GPIO with an external pull-up to PB2 on an STM32F413. It turns out that this pin has the additional function of being BOOT1, so the pullup caused the MCU to be unable to enter the system bootloader mode. I use CubeMX to plan my pin assignments, and this additional function isn't indicated anywhere in the user interface. Yes, I probably should have caught this by cross-referencing the report with the datasheet, but this is definitely an area where CubeMX should be able to help me out.
Amel N can you please pass this feedback on to the CubeMX team?