The STM32CubeMX code generation is not properly working in case the ADC is triggered by the HRTIM timers and DMA is used to transfer the ADC values to memory.
When the file stm32f3xx_hal_msp.c is created there is a missing line in function void HAL_ADC_MspInit(ADC_HandleTypeDef* hadc) which enables the DMA clock - ( __HAL_RCC_DMA1_CLK_ENABLE();
The STM32CubeMX generates code that enables that clock in main.c in a separate function called MX_DMA_Init(); But this is to late to configure DMA and make it work.
So with that extra line in HAL_ADC_MspInit everything is fine. Can you please fix that problem and offer an update so that everything works just out of the box.
PS: I really appreciate the STM32CubeMX. It is very handy