There frequently are discrepancies in square footage in listings at different websites. The county tax records give you a square footage based on the original footprint of the home when it was built. It only gets updated if there is a construction permit pulled for purposes of remodeling. In an mls listing, the agent gives their best estimate of square footage based on measurements of interior rooms, which is a guestimate. This is the reason that just looking a price/sq ft is misleading, because many other factors can come into play affecting the price per sq ft. It is always up to the buyer to verify what the actual sq footage is, and frequently the buyer relies on the appraisal done by the bank's appraiser for this determination. It is best if you look at the tax records, have your agent look at previous listings of the home, and ask the seller why there is a discrepancy--maybe they know something that is not apparent to others (like remodeling that was done without pulling a construction permit).
I hope this helps you in your determination.
Myke Triebold, GRI, SFR, LMC
Coldwell Banker United Realtors