Vol 7 - Sheol Fear, downplaying the strength of the nuns, removing the special way Agnese talks, downplaying Touma's entrance into the church. The only thing that didn't have any problems there was the last episode.
Vol 8 - removing the talk between Touma and Kuroko, removing Mikoto's ladde, removing LO revealing to Accelerator that she regained her memories, removing the scene were Mikoto knocks out Awaki's companions, the berserk Awaki scene didn't have disfigured appliances, making Awaki crash into a wall instead of a metal net fence, removing the scene where Accelerator yells at her while falling to the darkness of the ground (they made him say his speech while he was walking away), etc.
Vol 9-10 - Removing Himegami's monologue while she was down, shortening both games, QUALITY everywhere, more QUALITY, QUALITY fights, downplaying Touma's injuries and the way he figured out Oriana's attack patterns, downplaying Laura and Aleister's tense interactions, spell auras that make Touma look like an idiot, etc. The only thing they got right here is the Lidvia scene at the end. Oriana fight would have been good if they didn't have such QUALITY flashbacks.
Vol 11 - The entire 3rd ep. Rushed as fuck, and once again Touma's injuries were removed. They also didn't even hint at the long history between Venice and the RCC, and the nature of the guardian fleet and why it can't be dispelled by IB was not explained or even hinted at. Vento's scene with Matthai Reece was also shortened.
Vol 12 - My only complaint was that they skipped the scene between Touma, Tsuchimikado, Aogami and LO.
Vol 13 - First ep was rushed as fuck. Vento's attacks were also nerfed as fuck, the building she and Touma were fighting in had almost no people and it wasn't even close to collapsing. The Hound Dog's first encounter with Vento were also changed, making it hard to realize what was making everyone unconscious and removed one of Kihara's character traits. The Hound Dog massacre was not suspenseful enough, and it didn't highlight the fact that Accelerator was not in esper mode that whole time. They also skipped the conversation with the driver (removing characterization for the Hound Dogs) and shortened the conversation with Doc Frog, downplaying his experience, skills and importance. Second episode, Index's scene with the SISTERS was skipped, and also the way Index found out it was Kazakiri. Building toss was a joke, and the the wings didn't look like wings where you can see a clear division at the middle. Ahegao could have been better, and they skipped the hints that tell how Kazakiri was still fighting back against the control of the virus. 3rd ep, Vento's entire character motivation and the reason why she's using Divine Punishment in the first place was skipped, Touma didn't punch her nose, they didn't explain what the scales did, they fucked up the positioning in Kihara's office, they removed all the explanations that connect what the virus in LO is doing to Kazakiri to the Golden Dawn's method of creating an angel, and they didn't make the phone call scene as awesome as this. And then for the epilogue, they complete skipped Aleister's past, his plans regarding Accelerator, LO and Kazakiri, and Doc Frog being the co-founder of AC. The first scene there could also have been put in the place of the previous episode's ED. Then, they completely removed the open declaration of hostilities between the RCC and AC. I'm sure there's more that I didn't mention.