These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: Nakazawa seems to care very little for subtlety. Arguably justified, being based on the realities of wartime Japan, containing very little exaggeration.
Dirty Coward: The principal at Gen and Eiko's school. We're only given a brief glimpse of him in the manga, but what we see isn't very flattering. He's shown to be a spineless and weak-willed man who pretty much lets the militarist hacks posing as teachers pull any crap whatsoever at the school, including beating and stripping students half-naked over a spurious theft-allegation. He only - half-heartedly - berates Kijima and Numata, Gen and Eiko's teachers, after the two of them (as well Ryukichi, who made the bogus allegation in the first place) have had the shit beaten out of them by an enraged Daikichi over the stripping and humiliation of his daughter Eiko.
Harsher in Hindsight: The foreword in Volume 10 says, "Japan alone has over fifty nuclear reactors in operation. A missile striking one of those reactors could in effect function as a nuclear weapon, even without a nuclear warhead. Herein lies the true, albeit hidden, nature of 'peaceful' nuclear power. Whether triggered by an earthquake, accident or attack, it contains the seeds of horrific destruction." On March 11, 2011 a massive earthquake did critical damage to one of Japan's nuclear power plants and caused the largest nuclear accident since Chernobyl.
While the editor's words are technically true—the effects of a Fukushima-style disaster is functionally like a "dirty nuke," or radiological weapon—the implication that destroying or damaging a nuclear reactor would cause it to "function as a nuclear weapon" (like the type that was used on Hiroshima) is, sadly, Artistic License – Nuclear Physics.
Narm: The animated adaptation overall manages to convey hauntingly the horrors of war and atomic warfare... then Gen starts talking about the sorrounding debris and devastation rather casually. Also, his mother's giraffe neck.
Rooting for the Empire: Averted! Neither the Japanese nor the Americans look very good. Any insults directed towards the "Yankees" are probably done intentionally — it is written in the perspective of the Japanese — and it's not like the characters don't show any contempt towards their own country as well.
Signature Scene: When the first victim, a small girl, is melted in the initial blast of the atomic bomb.
Values Dissonance: Several. For example, Gen's father hits him and his brothers often as a means of discipline, and while it may be somewhat cringe worthy for modern audience, it's made clear that he loves his family and the practice was more acceptable then than now. To some, it may also be how hard Gen's father hits them. (This was fairly typical for western families as well.)
Eiko's strip searching would count as well.
Maybe not that, though. In-story it is very much treated as a horrible thing done to her, just a step below rape and a moral event horizon for their asshole teachers, as the theft-allegation was just a convenient excuse to punish Daikichi through his children. When Daikichi finally learns what happened, he understandably goes berserk as a result.