Spokes go further inside rim than others
On every single wheel I have built (and I have built 6 of them), the wheel looks mis-laced before the spokes have been tightened to the final tension, even though it was correctly laced. You tighten the spokes to the final tension and it starts to look like a real bicycle wheel.
One possibility is that you're seeing just this effect. Tighten the spokes more. If you cannot tighten the spokes enough, you have too long spokes.
Edit: on second thoughts, there is actually a possible issue you may have caused during the lacing. When lacing the first set of 9 spokes, it doesn't matter which hole you choose. When lacing the second set of 9 spokes, the first spoke must go to the correct hole. If you push a spoke through the test hole, you see that all holes in the left flange are inbetween the holes of the right flange. You need to select the correct hole: if the first spoke in the second set goes to the right side of the first spoke in the first set at the rim, the spoke hole at the hub needs to be just barely on the right side too. Not choosing this hole properly could perhaps lead to an issue where the spokes are regularly too tight, too loose.