I did find it strange that both series had a similar plot arc (to make a level 6) and both were connected to Misaka strongly, in Index very strongly linked to her history, and in Railgun by the associations she gains throughout the series. Yet none of the characters make any sort of acknowledgment in either series about having seen the wacky scheme before.
The other odd point would be the relationship between Misaka and Touma. From the progress, of sorts, that was made near the end of the series with the Aztec magician, Misaka's attitude in Railgun would make sense taking place some time before then. But if that's the case, does Railgun exist in that little window after Accelerator and before those events? Because we see no sign of the clones (as far as I can remember) in Railgun.
Or is this all just based off of a series of silly light novels/manga and I'm trying to apply to much wacky real-world logic to something that oughtn't. In the relationship question I suppose you can chalk it all up to silly anime romances where unless the author wants it to happen, no progress occurs.