I work in the industry, what more than likely the issue is, the vehicle probably comes standard with a 5spd,so the VIN number is decoding the vehicle with a 5spd. for alot of cars AT is an option, so does not show when the VIN is decoded. Unless the dealer goes in and manually changes the data that is being displayed, it will show the data the VIN number decodes with. The stock photos aren't meant to be misleading, with used vehicles they are normally used as placeholders till actual images of the vehicles can be taken. An add with any kind of picture has a much better chance of getting a sale then an add with no images at all.
There are tons of websites that will display basically the same vehicles that are from dealers lots, and then a variation of vehicles being sold by individual sellers. cars.com autotrader, and everycarlisted.com are three of the largest names on the web, but dont count out craigslist, you can get great deals thru that if you don't need financing. also alot of dealers use ebaymotors and instead of having to bid on the car, they will have the "buy it now" option which would be the same price normally as going on the lot and looking at the vehicles.