On the leg press, your lower back shouldn't move from the cushion in the down position. When the lower back begins to lift from the cushion, that's where the rep ends. It will tend to lift some more when you begin the concentric part of the rep, and it does tend to dislocate the vertebrae in the lower back.
Two things one SHOULD ALWAYS DO that directly alter these dynamics, making it more comfortable and safe to do the leg press.
1. STRETCH THE HAMSTRINGS. Every workout. They are the muscle that can cause among the most problems when they are not stretched appropriately. The hamstring attaches at the lower leg and also at the lower back, among others. This means that a hamstring lacking flexibility will directly pull on your lowest vertebrae when in the elongated position. It is an extremely long muscle group, overlapping TWO joints in the body, and thus has the tendency, like any muscle, to tense and shorten when it is trained for strength without proper stretching.
2. Strengthen the lower back erectors. In other words, DEADLIFTS. I have a "terrible" hernia in my lower back, and I deadlift without a belt and feel great. When I stop the deadlifts and reverse hyperextensions too long, pinched feelings return. Once strengthened, the spinal erectors can save your lower back from damage when put in a risky situation, such as going too low on the leg press...