GPIO is not working on Apalis imx6q

If I am not exporting the GPIO6_IO09 then the voltage across this pin is 0volt & when I am doing same thing with GPIO6_IO03 then it’s giving me 3.3volt.
when I am setting GPIO6_IO09(169-linux pin) pin as output and value is 1 then this pin is working properly.
But GPIO6_IO03(163-linux pin) is not working it remains to give me 3.3volt even after setting 0 to pin value.
The carrier board which I am using is customize and verified by bangalore toradex(INDIA).

Both Pins are by default on ALT5.

What exact software versions of things are you talking about?

By GPIO6_IO03 I assume you mean MXM3 pin 177 CSI0_DATA17 aka CAM1_D5 which is muxed as a parallel camera interface pin by default e.g. here. To use it as a GPIO one would need to first mux it accordingly as explained in the following article about device tree customisation.