Is this actually a thru axle bike, or are you just using that term for the quick release skewer? If it is a thru axle wheel, one or both of the end caps could be loose. A loose end cap can cause the wheel to slide from side to side on the axle, even if the thru axle is tight. It would not, however, cause the tire to rub the chainstay unless it has cup and cone bearings.