The difference depending on the position of the well

I am doing simulation of methane gas recovery using TOUGH 2 EWASG.  I created a three layer model of paleogene, cap rock, cretaceous in order from the top. I generated a methane gas from cretaceous and simulating recovery of methane gas collected under cap rock by digging wells from the ground surface. Without altering other conditions, the amount of recovered methane gas greatly changed when I dig well from cap rock to cretaceous point and from the ground surface to the same point, what is the reason for this?