SIM900A Strange Problem
Possibly when the SMS is sent the module draws large currents and the regulator is not able to support it and there is a voltage drop on MCU power linie or IO pin. (If module and MCU are running on same power supply)

SIM900A draws around 2A when network operation takes place.

Or possibly UART lines of MCU are shorted to IO input interrupt line. And when data is sent on TX line of MCU or RX line of MCU then that causes multiple interrupts to MCU and SMS are sent. 

Just a guess.