I found a bug in the latest version of CubeMX which causes the tick timer for HAL to be cleared in code if the corresponding timer pin is cleared.
Steps to reproduce:
1- Open project with any MCU.
2- Configure SYS to use Timebase source other than systick (here I use TIM14 for STM32F070F6)
3- Check that in NVIC "Time base: TIMxxGlobal interrupt" should be Enabled(and grayed out)
4- go to pin configuration and set one of the pins that timer uses for the timer output purposes(for TIM14 here we have PB1 TIM14_CH1) and select it. (we can't use the pin because HAL is taking control of the time)
5- reset the pin.
6- the Time base interrupt is now disabled in step 3 which should not happen.
I think sometimes it also happens if you configure the same pin for GPIO input/output but i can't reproduce it.