This is a hard question to answer because we can't see you performing this repair. How successful are you at doing other BGA IC's (Tristar, Tigris, PMIC, WLAN, BB) on the logic board? Is there a pattern in terms of IC size or location?
The biggest challenge to repairing an iPhone logic board is the thinness and component density. iPhone logic board are very thin, have ~10 layers of traces and have very high component density. What I suspect is happening is that excessive amounts of heat are bleeding over to adjacent components and IC's and you are probably creating shorts underneath them. By the time the Touch IC is at the proper temperature, you probably have half of the logic board at the right melting temperature as well. The CPU is very close and is smothered in underfill, when it gets heated the pressure builds up underneath and eventually the solder balls expand and can either bridge or explode out from the sides.
I usually cover adjacent IC's with a penny, nickel or dollar coin to sink some heat. If there are any FPC connectors then I will cover those with Kapton tape. I have a Hakko FR-810 station and I set it at 360-380C with the lowest airflow. Your station may require different settings. I also use a 6mm nozzle.
Let us know what equipment you use and any particular actions you take...maybe we'll notice something. This is where the "artisanry" comes in...you have to practice a lot to get just the right amount of heat to the IC and pcb but not more than you need.