Without seeing a picture....
Both fabrics HAVE to extend past the stitching line.
It's possible that you place the fabrics correctly, but when you turn it over to stitch on the line, something shifts.
Happens all the time. ;-)
Try pinning the fabrics after you've placed them correctly. Be careful when you flip it over that the two fabrics are still laying flat (without tucks or folds) before stitching.
And I wouldn't be taking the paper off until the block is sewn together with other blocks (or the whole quilt top is completed), depending on the pattern.