Start with new CubeMX project, selecting NucleoF303ZE board. Enable 1 single ended channel on each of ADC1 and ADC3. Select Regular Conversion Trigger for both.
CubeMX generates this line in MX_ADC3_Init():
hadc3.Init.ExternalTrigConv = ADC_EXTERNALTRIGCONV_EXT_IT11; // incorrect
IT_11 is incorrect for ADC3, it should be EXT_IT2
hadc3.Init.ExternalTrigConv = ADC_EXTERNALTRIGCONV_EXT_IT2; // correct
.ioc file attached.