No, I don't think so. "Duplicate entry" simply means that those lines it showed are written at least two times in the reposity files; apt-get doesn't do anything with identical duplicate lines, so it warns you that there are unneeded lines there (which just take up space from the file).
If you don't want to see the error message all the time, you can simply go trough the reposity files and remove all duplicate lines.
If you want that easily done, you can do it with uniq. It's a tool to remove duplicate lines; command works like
uniq infile outfile
where uniq reads 'infile' trough, removes duplicate lines and puts the output to 'outfile'. So just feed the reposity files to uniq (one by one, unless you want to script) and copy the output over the input. Probably just as easy is if you open Synaptic, reposity configuration and scroll trough the content, removing duplicate lines if you happen to see any.