Strange Foot Pain

I'm fairly new to structured climbing (shoes, harness, etc rather than just climbing buildings and structures around town). I went and tried shoes on before I bought them and everything felt fine. I even got up on a wall the store had to try them out. I've only worn them twice at the gym. I noticed something strange about half way through climbing...
When I land from boulders or stand on my toes and then put my feet back on the ground, air bubbles pop out. It is the same spot on both feet. Along with the air bubbles, I get bad pain on the outside of my feet. Now my feet aren't the most normally shaped feet around - from the outside of my feet down towards the ball of my foot area, my foot dips ins. This is the same spot where the air bubbles occur. The pain in my feet is just above where the bubbles occur.

Is this a problem with my shoes, my feet, or something else? Is there a way I can fix this (such as stuffing that area to prevent bubbles)? Or do I need to get all new shoes?

Thanks for the help.

Not sure if this is a troll but.. Are you wearing a synthetic shoe?

Nope not a troll. Completely serious. No, the shoe isn't synthetic. It's leather. They are Scarpa Helix shoes if it makes a difference.

Funny, my feet dip in at about the same spot yours do if I'm reading your description correctly.

Are you tightening the shoe laces carefully so that the shoes follow the contour of your foot properly? That might eliminate the air bubble. It might also provide a little extra support to your feet, and reduce the foot pain.

I'm not suggesting that you just crank hard on the laces and get them as tight as possible. I'm suggesting that you work your way up the laces from the bottom eyelets, getting the shoe as close to the foot at every point, so that there are no voids or air pockets in the shoes.