Wrinkles in the finished product occur for two reasons: an excess of surface area in the plastic, or tall products spaced too close together.
In the first instance the problem can be solved by simply reducing the amount of preheat time in the film cycle. The drape or "belly" that the film has after being heated, but before lowering to the board should be about 2" for normal products. If your drape is more than 2" it creates extra surface area that results in wrinkles.
The second case is a bit more complicated. Because the film is trapped around the outside edges of the film frame, air is removed there first by the vacuum, resulting in a outside-in movement of the plastic vacuum cycle. The plastic will shrink in the shortest direction unitl a state of vauum is achieved. The ideal direction is vertically, or down to the paper. If however, two tall parts are too close together, this direction will be horizontally. This creates a "web" of plastic between the two products. This can be fixed by moving the parts farther apart. Another fix is to string a wire between two opposing sides of the top film frame that will run between the two products. The wire will drive down the plasic in between the products and ensure a acceptable seal.