This may be a link to the pattern. It looks like the pattern is knit in pieces and sewn together. The comments in the projects also read that way. You might try putting the decreases one or two stitches in from the edges. Then when you seam, they should line up nicely. As Sue mentioned, blocking may help even them out too. There's videos for k2tog and ssk on the Glossary tab at the top of the page in case you'd like to see.
It's a darling sweater that will look adorable on the baby!