What is the minimum amplitude level of the input signal to trig the capture interrupt in xmega timer
This is usually specified as the Vil and Vih voltage of the GPIO - the maximum voltage guaranteed to be read as zero and the minimum voltage guaranteed to be read as logic one.

For example http://ww1.microchip.com/downloads/en/DeviceDoc/Atmel-8067-8-and-16-bit-AVR-Microcontrollers-ATxmega64A1-ATxmega128A1_Datasheet.pdf section 34.10

Check your signals with a scope.