This page offers a good look into what’s called natural gas migration. This is an occurrence of the gas escaping from the rock reservoir, a pipeline, a well or a coal seam. If you read the info at this link you’ll find some explanation for some of the problems people have been having with methane leaking into their homes and water wells.
As far as my personal experience goes, I know there have been cases of water wells contaminated by methane gases in Tioga County before the gas drilling began in full. For this reason I think it is very important to make sure you have your water tested prior to having a well put in. If your water was fine before a well and after the gas well is put in you have problems with methane, it will be tough to prove this to the company who drilled your well with out having a water test that is dated prior to the gas well. I would attempt to put something in a lease agreement that has the energy company pay for the water testing as well as be responsible for fixing any problems that arise, including the methane gas.