It's the VMs garbage collection. You can't avoid it, it's a basic concept of a Java VM. You can reduce it though by reducing the number of object creations at runtime. What causes these object creations highly depend on your app. jPCT-AE itself is very conservative when it comes to object creation. If you are methods that return a Matrix or a SimpleVector, consider to use the variants that take a "toFill" object instead. More info here:
http://www.jpct.net/wiki/index.php/Performance_tips_for_Android#Avoid_object_creations
