Okay, when you go back to the green after the little squares, the first row of the green, you will be on a knit side of the work. As you work this first row knit the two green stitches and purl the two that are over the blue stitches alternately all across the row. Then on the purl row, just purl back across over all of them and you are back to your reverse stockinette.
This will make one row of green that is knit above the blue blocks but it won't be noticed and the only alternative is the result you are now getting. This is the way a clean edge is made on the color in this kind of situation. If you were making just a normal stripe you would knit the whole row to change colors but with the alternate colors you will do it this way.