This has happened to me on several occasions. I use what they call in embroidery the ladder stitch. You bury your knot take a small stitch vertically close to the edge, than another one directly opposite and than another one back next to the first on (like a ladder ). after a few of these stitches, hold your thread and pull. The edges of your seams will pull under and make a nice neat closing. I learned this stitch from my neighbor who makes dolls for a hobby.
Hope you can understand this and it helps