07 Highlander, abs, trac and vsc lights on???

I took the vehicle into Toyota...they said the lights were on because of a failing hub bearing assy which caused intermittent operation from the center of the right rear speed sensor...so I had the hub bearing replaced at another shop. they tried to clear the codes but none are showing up. now not only do I have the three codes...but I also have a low tire light on. any ideas what might be causing this?