if your truck has never had an alignment then it likely has the factory retainers on the camber adjusting plate on the control arms.
some places <insert adjective describing such place> will tell you camber/caster cannot be adjusted and/or they will only set toe and pass it off as a completed job. So my initial guess is all they did is was set toe and bill you, and say the problem is because of modification.
the second likely problem and i don't know if a 3" lift is enough to cause it is the camber/caster has been adjusted but there's not enough to allow for your 3" lift. This should have been stated in the lift kit you bought for your truck, and whether you need to buy extra suspension parts to make it work.
the other big problem is if you break out the factory retainers and adjust the control arms to get caster between +3° and +5°, and camber between -0.1° to +0.7° which are ballpark acceptable ranges, you need to make sure the ball joints are still centered enough to allow for suspension movement. Because at some point you can also max out how far the ball joint can angle, then when the suspension travels upward if the ball joint has no more travel you'll break it... then crash. The ball joint problem can be fixed with new adjustable/offset ball joints which allow for greater adjustment of the control arms to get camber/caster to the desired value but not max out the ball joint.