At some point everyone has experienced poor design registration. Often, one has a large fill edged with a column or satin stitch, and the fill and its outline do not meet. The first thing you need to determine is, was the design digitized correctly for the material you are working on. An experienced puncher positions the column stitches more inside or outside the fill. This is called pull compensation, and it makes the column sew exactly where it should when running on the specific fabric it was punched for.

Improper hooping and using the wrong backing are two other common causes of poor registration. Creating the correct fabric tension in the hoop is critical for good registration. The sewing field should be taut, but not so tight that it will alter the garment when it is removed from the hoop. Hoops that are too tight may cause the fabric to stretch out too far, creating a bagging effect, or it may cause hoop burn. Hooping too loose will allow the fabric to pull loose form the hoop while being embroidered, causing poor hoop registration.

It is important to use just enough backing to stabilize the design area. Experiment to see which backings work best for different jobs. Talk to experienced embroiderers to see what kind of backings they use for different applications. It may help to keep a record of these findings for future reference.
As one final note, make sure the backing is completely engaged by the hoop to ensure an even tension in the sewing area.