I'm going to reserve the judgement on the anime as a whole, primarily because I'm a victim of "poisoned by manga" syndrome. But to pick on one most unpleasant lapse, my favourite segment of visiting the candy store was butchered. In the manga, the pacing and fidelity were excellent. It was easy to believe it happening. In the anime, it did not work so well.
To start, Hotaru's fascination with Komari-semai's cuteness was not as well established. In the manga, Komari was given the natural cute that blossomed gradually. In the anime, they moved the segment way ahead into the 2nd episode, therefore having to explain the setting instead of showing it to us. Komari did not have enough screen time and did not behave in any "cute" way. She was a complete a non-entity until the sudden revelations.
The episode itself seemed clumsily made, too. In manga, Hotaru (perhaps accidentally) hit just the right note with her attire which projected the adult as imagined by a middle-schooler. In anime, they re-dressed her way down into something that an real-life adult would wear. I do not think Komari would fall for it in character so easily.
I'm not a big judge of comedy, but something was even off in the comedic timing, so that the 10-man note lost a lot of its power. The shock was demonstrated to us with Komari's reactions instead of being felt directly. I am willing to cut them slack on that. Adding or removing half a second of screen time would improve it a lot, perhaps, and it's tough to accomplish. But this definitely was something the director has a duty to control.
The only moment that worked, I think, was when Komari was wondering how she went along despite having expressed her reservations about strangers. Let us give the creators 15% of success for it. The score is not the second coming of Azumanga.
UPDATE: Peter S. calls the candy store trip "a less-successful part", which "wasn’t very funny".