Sniffing for Gas and Oil

I just finished the March 22, 2010 edition of Time Magazine.  An interesting Shell Oil ad appeared titled "Sniffing the Air".  The article tells of their new technology whereby they attach sensors to planes that fly at approximately 1,000 feet above the earth's surface.  These sensors have the ability to detect methane and ethane gas that is emitted from cracks within the earth's surface. Did I say cracks?  Funny, they claim that these reserves can sometimes be miles beneath the earth's surface.  Is it possible that this is the same gas and oil industry that also claims that our aquifers are safe?   I thought the fairy tale went like this: because all toxic chemicals are injected at least a mile beneath the surface that it's impossible for those toxins to migrate into the acquifers.  Then how do those ethane and methane gases bubble to the surface from miles below?  Do I see a disconnect here or what
Below is one article about this subject from Forbes and another is a document from Shell Oil in pdf form in which you need to go to page 20 and 21. This  photo is from the Forbes article below.

http://www.forbes.com/2010/01/21/airborne-oil-detection-technology-breakthroughs-shell.html


http://www-static.shell.com/static/innovation/downloads/ep_technology_magazine/EP_Technology_2008_3.pdf