That's the pro/cons of being an anime only watcher. Many manga readers disliked S1 for being anime-original and now with S2, many anime-only people feel like they're missing the "original" humor that the show had before. JC Staff is doing a rather loyal adaptation of the manga which many people like now however.
A lot of the "plot holes" in S1 are because there was a lot of anime-original material and it jumped around chronologically a lot. This meant that some people like Ayumu's brother got left behind etc in S1. With episode 52, they did a time jump, pretty much.
The trip occurs later in the manga, and the anime isn't up to the point yet (s2).
Regarding the train thing, the first episode was anime-original, the one with Ayumu's brother was in the manga.
Regarding the Hina and Ayumu thing:
Episode 48 of S1 was a bit of a stretch between canon manga stuff and anime stuff. In the beginning of S2, think as if nothing really happened in S1 honestly, aside from the actual manga material. My last point is that, S2 starts off from the manga material that S1 never did and moves forward from there. I love the anime, both seasons still, and the manga's great. I find it better to be an anime only watcher at first and then jump into the manga so you'll see how everything flows together but too late for me now.
That was a long post, lol. Looking forward to S3 now, maybe in 2010 hopefully