There are several things that can go wrong, causing the panel to be non-flat. The most common problem that hinders me is that the stock itself can have a slight cup, twist, or bow to it. Occasionally I will miss an imperfection in one board, and the imperfection becomes more pronounced as the board becomes part of a wider panel. If this is the case, you may be able to cut the offending board out and replace with a better one by re-gluing the panel.
Another thing that can cause problems is too much clamp pressure. This is a controversial point, and many woodworkers will say that there is not such thing as too much clamp pressure, while on the other extreme, I have heard of some who perform edge gluing with no clamps at all. I am somewhere between the two extremes. I have had more consistently flat glue ups since backing off on the vein-popping clamp pressure.
Another problem is imperfect alignment of the panel. Be sure that all boards are planed to the same thickness, and be sure to force the boards flat to the clamps on the bottom. If they boards slide up the clamps from pressure they can cure in that position.
One more possibility is improper jointer or table saw setup. If your jointed edges are not a perfect 90 degrees, this will cause you problems which become magnified over multiple joints in the panel. The best way to offset this is by marking the top of your panel, and then alternating the face that you run against the jointer fence. For each joint, you want to run one top of board, and one bottom of board, against the jointer fence.