I find that most people, who are not used to lead came, cut the crossing pieces too long so the whole panel grows. Each piece of came that is a fraction too long pushes the passing came out, making the glass apparently too large. You can and should make sure that you have pressed the came snugly against the glass. If the next piece of glass you place goes over the line allocated to it, something is wrong with the previous piece. Undo the came and check the size of the glass against the cartoon. If the glass fits inside the lines allocated, the problem is the way you have fitted the came to it.
Another check you can do is to run a felt tip pen at the side of the came onto the glass. Take the glass out and examine the space between the line and the edge of the glass. This will tell you where the glass and came are not fitting equally. A narrow space does not immediately mean the glass is too large, it may mean the calme is not tucked against the glass properly. So check that first, before any grinding.
Nails, push pins or other things that you can push into the work board will keep things stable. If you are working with a rectangle you can use wood battens. If not, multiple close spacing of nails will help. Also you could cut a piece of glass into a shape that will hold the outside of the panel.