The aswer is two fold. A legitimate price difference would involve upgrades or additions, e.g. new cabinetry, plumbing, roof, or bathroom, pool, location, lot size etc.
The other part is an over inflated price, usually due to what the seller wants to make on the sale of the home, or the seller paid too much for the home and could be in a pre-foreclosure situation.
Some upgrades can warrant a higher sq. ft. price while others, may have additional features but not necessarily price inflators. What I mean by this is, 2 t.v.'s are selling for the same price but one has a built in DVD player. That would be considered a feature.
If someone is desperate to sell, they should reduce the price significantly and that would lower the sq. ft. price too. The list price divided by the heated sq. ft., will give the sq. ft. price. If they lower it by another $5,000, the sq. ft. price will obviously decrease.
Hope this helps.