If the
scene is in the Gundam Seed manga it will probably censor that though I'm unsure if that was in the Gundam Seed manga. Also some of the heavy bloody violence later in that series.
The dialogue changes didn't seem that severe to me. The one on the train fit since the girls were teasing him in the manga anyways. It's actually more like they moved the sex joke from the bottom of the page to the top really. The cookie joke was a bit more serious though since it makes negi look goofier and more like keitaro which is the main thing that sits negima apart from love hina (the lack of the perverted loser main character typical to this genre). Hopefully will be no more of this in later releases but if they can keep it to one small gripe a manga and keep it uncensored (wasn't even anything to censor really) I'll be happy.