it could also be there are too different plasmids there...it is not easy to get rid of it...do transformation with very diluted plasmid DNA...I ran into a similar problem once but it wasn't a problem for my cloning, i never bother to do anything with it...
Bingo LZ please refer this paper reported method: Balagurumoorthy et al. (2008) Method to eliminate linear DNA from mixture containing nicked circular, supercoiled, and linear plasmid DNA. Anal Biochem. 381: 172-174. link: //www.ncbi.nlm.nih.gov/pubmed/18638445