Hi Hugo,
To clear the SRC_FF_MT interrupt status bit in the INT_SOURCE register (0x0C) and consequently deassert the Freefall/Motion interrupt, it is necessary to read the FF_MT_SRC register. Are you using something like this?
void PORTA_IRQHandler()
{
PORTA_PCR5 |= PORT_PCR_ISF_MASK; // Clear the interrupt flag
Temp = I2C_ReadRegister(MMA8652FC_I2C_ADDRESS, FF_MT_SRC_REG); // Read the FF_MT_SRC register to clear the SRC_FF_MT flag in the INT_SOURCE register and deassert the interrupt
MotionEventCounter++;
}

Also make sure that your GPIO pin connected to the INT1 pin of the MMA8652FC is configured for falling edge interrupts.
I would also recommend to start your experimenting without using the Auto Wake/Sleep function (CTRL_REG3 = 0x00), with only the Motion/Freefall interrupt enabled (CTRL_REG4 = 0x04) and routed to the INT1 pin (CTRL_REG5 = 0x04).
I hope it helps.
Regards,
Tomas
PS: If my answer helps to solve your question, please mark it as "Correct". Thank you.