The second halves of the first two seasons of A Certain Scientific Railgun seem to contain content not seen in the manga. Are they considered filler and thus not canonical to the overall plot of the Raildex Universe? In particular, I am asking whether the Silent Party Arc (Season 2: episodes 17-24) and the Poltergeist Arc (Season 1 17-24 + Season 2 episode 1) are canonical.
First, let me say I am personally not inclined to offhandedly label anime only content as non-canonical. That being said, I do believe these two arcs introduce some problematic elements.
One problem I see is the theme of the power of friendship in these arcs, which is much more prevalent than in arcs from the manga. Namely, Mikoto Misaka teams up with all her friends to try and solve the problem. This is problematic because this "lesson" Misaka seemingly learns here that she should trust her friends... she doesn't actually learn it. Elsewhere, she maintains her prerogative to go solo and keep her friends out of it. This is particularly true after the Poltergeist Arc, since it is followed immediately by the Sisters Arc. But even after the Sister Arc, rather than with her friends, Misaka seems more willing to team up with
Shokuhou, a fellow level 5 esper.
particularly when the dark side of Academy City is involved, to keep her real friends out of danger. Also, as a side note, the ending of the Silent Tea Party Arc might be more than a little surprising to anyone not already aware of this relationship. And Misaka seems a bit resistant to and also remorseful about involving Kongou in the next arc, saying in volume 8:
Whatever you do, don't get too involved. I don't think you'd be in any real danger, but I also don't fully know what she's capable of.
Be careful, Kongou-san... This isn't your problem, so please don't get hurt.
Evidence For Being Canonical
Moving on, we can get into actual evidence for and against. As far as the Poltergeist Arc goes, Haruue Erii does make cameos in the manga, thus proving her existence and relationship to the main characters. Uiharu is talking to her on the phone in Chapter 31. She says:
Haruue-san said she'd meet us after she visits the hospital.
Erii again appears in Chapter 32, in a picture on Misaka's phone. The picture seems to be from an event in the anime, according to the trivia section on Erii's wiki page.
Evidence Against (Timeline Inconsistencies)
A lot of the argument against the Silent Party Arc being non-canonical stems from Kongou and her two friends being involved in the arc. Kongou is actually introduced in the arc after the Sisters Arc, and she has just transferred in to Tokiwadai. However, from what I recall, this inconsistency seems to be a problem with the entire first two seasons of the anime. I'd have to verify what differences there are in the third season and the manga events.
I'm also seeing claims that someone on the Railgun anime team disavowed the Silent Party Arc in a tweet as a "mistake", though I have yet to track this tweet down.
Anyway, draw your own conclusions about whether these arcs are canon from the information available. I'm not going to say it is or isn't canonical, because that's subjective.
Note also that the two episode Big Spider Arc is also anime exclusive, though it's wiki page states it is considered canon (without any explanation). I'm not going to go into it, but it's obviously relevant here.