This HINT is for when a design stitches great except for one or two small gaps between sections. If the gaps are very small and color is darker than your fabric you can use the appropriate color in a permanent marker to fill in the gap. It is better to make several small marks than one big one to look more like stitches.
If the gap is a little larger or the color is light and a marker won’t work, you can use your regular sewing machine. Thread the missing machine embroidery thread used in the design onto your regular sewing machine. If you are comfortable doing free motion stitching, stitch back and forth in the gap following the angle of adjoining rows of stitches.
If free motion isn’t for you, thread your machine as above and do a few rows of stitches to fill in the gap. Follow the angle of the design stitches and go very slow so you don’t over stitch. The goal is to fill in the gap, not cover the gaps edges. Experiment on similar fabric to see what stitch length looks the most like the stitches. 