If the worked on the bottom bracket only, they probably did not remove or even touch the rear wheel at all. However, a good shop would give a bike a look over during the ticket writing and point out an obvious problem...and then ask if you wanted it repaired.
A mis-mounted wheel can rub, as can a off-centered wheel. For wheel truing see
http://www.parktool.com/repair_help/howfix_truing.shtml