To be honest I've rarely had a sheet that is completely flat, even the thicker 6mm stuff and have had to be selective where I cut larger items like keels from. For formers/bulkheads it isn't usually a problem as a slight warp isn't much of an issue, even visually.
But if you have had to score it then your ply must have been seriously warped! Trouble is, particularly with Liteply you are reducing the strength by doing that, which isn't that great in the first place compared with other types.
Chris