Too much glue`
I also had this problem with my first kit. I still use wax paper but I now use alot less glue just as flap described. I apply just enough to tack the joint and after removing the part from the board I apply more to all sides of the joint. If you use too much CA and in flows out the bottom of the joint, even if it doesn't stick to the wax paper or plan protector, it still will create a hard spot that will be difficult to sand off later. Another tip is to use the glue tips (pun intended) that you can get from tower hobbies or your LHS. They make it much easier to control the amount of CA that flows out of the bottle.