There are even more problems with the Railgun anime than just that.
1. Complete inconsistency with the actual timeline. Railgun's anime fucks with the timeline. It's as if it wants to ignore the fact that Index is a thing. From how the Level Upper Arc was adapted to Silent Party, there are inconsistencies everywhere. Funny enough, I honestly think that Nagai, the guy who directed Railgun, has zero respect for the source material that he was adapting. I think he was even on record as saying that he did not want to adapt the Sisters Arc.
2. Flanderization. Oh god. Flanderization. If you want any good examples, look no further than Kuroko, who is an incredibly likable character in the source material but completely unbearable in the anime for the following reason. The damn anime took her occasional perverted outbursts and made them the centerpiece for her character. Do you think the director had any respect for the source material?
3. Cutting out scenes or adding in scenes (both of which derail character at times).
Example 1: There was a quick scene in the manga that was cut out that ended up being quite a humanizing moment for Kiyama during the car chase, showing her to be more of an airhead than evil.
Yet, it was cut out because Nagai wants to portray all of the villains as evulzeeeeeeviiiiillll...
Example 2: In Railgun S's Sisters Arc, (yeah, even Railgun S's Sisters Arc had its fair share of irritating issues) there was a scene in the anime where Accelerator was chewing a finger after he killed a clone. THAT SCENE SHOULD NOT HAVE BEEN THERE! There was a scene where Accelerator did chew a finger but the context was entirely different. In the novels, Accelerator was chewing Misaka 10031's finger in front of 10032 for the sole purpose of intimidating her. He was trying to get a fear reaction out of her by continually escalating his intimidation and if you have watched or read Index you know exactly why he was doing it. In Railgun S, the scene seems like it was just there as a 'for the evulz' moment.
Yeah. Railgun's anime was...a disaster as part of ToAru.
Here is a list of problems with the adapted arcs that someone on reddit made:
https://www.reddit.com/r/anime/comments/3hi4ky/spoilersa_certain_scientific_railgun_s_episodes/cu7k0ug
This covers Railgun episodes 1-12 and Railgun S episodes 1-16 as they are the adapted arcs.
And here is the same guy pointing out a number of problems on the episodes of Silent Party:
Episodes 17-18
Episodes 19-20
Episodes 21-22
Episodes 23-24+Overall Summary
Yeah. Is it any wonder people think Nagai has zero respect for the series he was working on?\
EDIT: So, I've been doing this little thing where I'm analyzing the character arcs of the main characters Volume-by-volume. Take a look if you're interested.
Kamijou Touma-Volume 01
Kamijou Touma-Volume 02
Kamijou Touma-Volume 03
Kamijou Touma-Volume 04
Kamijou Touma & Accelerator-Volume 05