I was wondering why when I run a VIN on a vehicle it says it's an automatic,but when I went to drive it,it was a standard.Should this be a red flag?

Verify the VIN on the dash and the title, first to see they match and second to verify you had the correct VIN.

Denise look on driver's door jamb, should be a data plate that gives transmission code: see this link: http://www.lcengineering.com/LCTechPages/TECHGEARJANUARY.html - the data plate will show tire sizes and tire pressure, vehicle weight, transmission code, and differential code. A/TM for automatic, A34OF being the most common for Tacomas. This link will give you engine serial code locations, the last several digits of the serial number should match the last digits in the VIN code: http://www.toyotaparts.metro-toyota.com/ENGINE_SERIAL_NUMBER_LOCATION_T-SB-0301-08.pdf