I think you are cutting over the lines.
Anything pins or tails first, then the other you will mark according to the first pins or tails. After that it is better for you saw the second pins or tails with the lines remained just a little. In the corners, you have to remain the lines otherwise you cannot match the two. Even if you remained the lines in the corners the corners are not match, you have to align the bottoms of the pins and tails. check the bottom lines with square ruler if it is straight and match the knife line. I think you have remained some of wood in the bottom. Then the corners will not match well.

Good luck

Shon