A trainer should acquire your consent before touching you in any way.
This should be common sense, but apparently it is not. I have done some personal training, and there can be times where touching the athlete, for example to help demonstrate a movement pattern, can be helpful. But I always ask the athlete, "may I put my hands on your elbows?" or whatever I am trying to do, and acquire verbal consent from the athlete prior to touching them at all. In your case, standing on the athletes toes is pretty common for providing assistance with sit ups, though I have never had an athlete mention pain, and again, I have always asked the athlete prior to doing so.