Do you mean that the stitches are facing you incorrectly or that the stitch holder is backwards? The latter is just a matter of slipping the stitches to another needle.
You should have the front and back joined at the left shoulder, and as you go from the front to the back, stay on the right side.
Is it possible that the back was reversed when you attached the shoulder?
Can you post a picture?
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IngridKH on Ravelry