It appears the complex elements were created from a MicroStation complex element. To be clear our civil elements are basically MicroStation elements with rules (and gaps / intervals)
Im not positive what caused this. It could be the base geometry had an overlap, or it could be a relationship was broken at some point as I see a number of broken relationships in the file. Some of these may have been because I did not get the attached references.
To delete the problem alignment follow the video attached..
http://www.screencast.com/t/OacKBuZ5
The steps are
1. Open the 2D Model
2. Use the "Drop" command and drop the complex element
3. Delete the elements
HTH
Mike