First two answers are spot on. It won't lay flat. It is not supposed to.
Another job of darts are to make something fuller without gathering it. I made a Barbie doll ballgown with 6 darts in the waist of the dress. Barbie's waist is teenie tiny looking, and the dress goes poof at the bottom and stays that way. No bunches of gathering at her waist, the dress bottom stays perfectly round, as if I had put a cage in it.
When you set in dart, and especially with fabric that stretches, you have to be exact with the dart. Pin it profusely, sew it with a steady hand, and check and double check that the marks you made to sew with match up exactly. Elsewise you get a slightly scewed dart that will not do its job. And, it will not lay anyway: straight, flat, or on a curved you.
Use dressmaker's chalk, mark the whole dart. check it. Fold it to prep it for sewing, pin it good, and check it again to make sure it is right. Sew it, take out the pins, and make sure it came out right.
Trim the seams, clip it so it will curve with your curves.
And make sure your seam is straight, Nothing worse than a dart that is rounded at its slim end. It makes a bunch on the fabric, and on you.
Your only other choice, if you do not want to dart the short, is to gather the waistband, and put elastic in it. the shorts will then curve, and will at least bag properly.