Like Tom said, check the holes. Shine a light down in there and see if there is an allen screw or something down in them.
An easy way to shorten the screws you have is to use a nut with the same threads (if you have one). Just thread it on and grind or file down to the nut and when you back the nut off it will chase the threads.
If you know what the threads are, you can get shorter screws at any hardware store or try a local gun shop/gunsmith.
They probably just sent the wrong length screws. I had that happen with a single shot rifle that came with a base and screws. They were all 1/4" too long and bottomed out in the holes. Ground them down and they worked fine.
You could also use shims under the bases. You can get the stock at Lowe's.
Good Luck.