I used MN NucleoBond Xtra Midi to extract plasmids, but the agarose gel electrophoresis showed the plasmids contained not only one component. There are bands around 250bp, what are those bands?
I would suggest RNAII-like priming RNA related to the initiation of plasmid replication in bacterial hosts. Part of it might avoid RNase digestion when it forms a heteroduplex with plasmid DNA. Then, it will co-purify with the plasmid assuming standard miniprep protocol. The RNAII size could be within 300-600 nts range unless Rom protein or alike is involved in termination.