How can I patch holes in the crotch of my Patagonia Trail shorts.

All of my Patagonia Trail Shorts develop holes in the crotch, usually within a year of purchase. This is after the liner disintegrates, usually within 6 months.

I love the trail shorts, they just don't last in the crotch. I usually just cut out the liner, but eventually the outer layer's crotch-area also develops large holes. Is there a way to patch these?