I strongly suspect you have mis-connected things. To be sure I would need to see your PCB design files.
The pins can be changed, see the start of the sketch:
const byte CT_SHUTTER_PIN = 12;
const byte CT_FOCUS_PIN = 11;
const byte FT1_PIN = 10;
const byte FT2_PIN = 9;
const byte FT3_PIN = 8;
Just change the above to suit what connections you want. Please note; if you upgrade the sketch you would need to change the pins again.