It sounds as if you may have incorrect hardware. The hangars/rollers for the front and rear of by-pass doors have differing amounts of offset. If is this is the case, you should return them for correct replacements. However, I don’t suppose you have just hung the doors in a reversed position, have you?
You will not find shorter doors. You just need to trim the bottom of the door to fit your opening. I have on occasion trimmed hollow-core doors to the extent that I got into the hollow area. When that occurs, I just fabricate and glue in a small filler piece from some scrap lumber. It works as good as ever.