I have had this happen a number of times and sadly they generally are mutants that don't flower properly or have a very high chance of being hermaphrodites.
These days I now cull any twin seedlings due to my previous bad luck when growing twin seedlings.
Hope this helps, Organoman.
P.S. - I hope you have two separate grow spaces, as growing autos and photoperiod plants in one grow space is going to be a problem. Your photoperiod plants won't flower at 18/6 and your autos won't produce much at 12/12.
If you are growing outdoors, then no problems, but the autos don't really perform that well outdoors in my experience.