I had that problem before. In my case it was my fault entirely. I got into jumping position before his legs left the ground and wound up having him jump early.
I know I'm going to get a lot of comments saying that you should never do this, but it worked for me. With bigger jumps, you can actually feel when the horse is going to jump. With smaller ones, you have to be expert to feel it. When I started jumping, I always sneaked a quick glance at the jump a stride or two away, so I could 'guesstimate' where my horse would jump. I put that mental image in my head and then looked ahead, so I'd know when to 2-point.
Sit deep in your saddle as you aproach the jump. As soon as you feel your horse lift off the ground, 2-point.
Hope I was helpful :)