TIM 2 PWM Input on different pin STM32F072B Discovery
This is because only specific pins of each port can have a function, in this case the Timer2_Channel2 is assignable only to PB3, and PA1 on this specific processor (STM32F072xB); see page ~43 on http://www.st.com/st-web-ui/static/active/en/resource/technical/document/datasheet/DM00090510.pdf

Thus the pins did correctly configure as input, however they did not connect to the timer.

Its a little sad that this doesn't have static control.