In the anime Excel is willing to kill for Il Palazzo right from the start; meanwhile, in the manga, she struggles with killing a rabbit for dinner.
In the anime Excel is all too comfortable to try eat Ms. Mince at any given emergency while in the manga just bringing up the idea fills her with guilt, even if doesn't really dissuade her.
In the anime the weak and usually harmless Hyatt doesn't even think twice about following Il Palazzo's orders to kill the neighbors, specifically Watanabe even if she fainted before doing so, yet she blatantly disobeys his orders to forget about Excel by giving her a trace to find and a way to enter the ACROSS fortress.
Or could it be that she thought bringing back Excel was the best for Il Palazzo?
Designated Hero: Excel does heroic things from time to time, but she is still working for an evil organization. Meanwhile, the City Defense Force (particularly Iwata) think they are working for the good of the city, but do as much harm as good.
It's more mixed-up in the manga, where ACROSS doesn't really qualify as either good or evil organization (the world is definitely just as corrupt as Il Palazzo declares, though he's hardly the best person to fix the matter), while the civil servants really have no illusion about Dr. Kabapu's morals (or lack thereof), either.
Author's Saving Throw: Revealing that Dr. Shioji only likes to watch little girls because it gives him some sort of peace, instead of being a full-blown pedophile, just as he was becoming more important to the main plot, was so this. The expanded explanation is that his mother left him with a skewed view on adult women, but he was inspired by the innocence of his young cousin; now that she is grown he is simply trying to find that inspiring innocence elsewhere.
Near the climax of the manga, Shioji finds out that his "mother" was a third Ropponmatsu unit built by his father, and at the very end it appears that he is coming to terms with his foibles - he acts far more mellow and appreciative of Umi.
Les Yay: Excel and Hyatt, obviously. Also, Elgala gets very touchy-feely with Excel when she's drunk, even though her "innermost thoughts" claims that she does not swing that way. Excel invariably retaliates with violence.
Anti-Climax Boss: That Man took half the series to beat, while the other members of the ACROSS Six are beaten in a quick gag in the final episode.
Better on DVD: Behind all the frenetic hyperactivity and deluge of jokes and references IS an actual ongoing story that develops from episode to episode with some surprisingly intricate detail, and it's much easier to catch while viewing the episodes close together. Not to mention, the ADV Films release included "AD-VidNotes", their version of Pop Up Video, that explains the many obscure references.
Crosses the Line Twice: Episode 26 (titled "Going Too Far" and intentionally designed to make use of this trope), as well as anything involving Shioji.
Fridge Horror: When Ropponmatsu II starts acting rather intrusive towards Excel, we see Hyatt watching the two before the Relax-o-Vision starts. After that, we return to the same shot, with Hyatt sitting in the exact same position, apparently having watched as Excel lost "... a bunch of things".
Genius Bonus: The references to obscure anime. Unless you're incredibly well-versed in anime from the '70s and '80s, chances are at least something will go over your head.
Les Yay: Besides one episode entirely dedicated to parodying the Yuri Genre, Excel and Hyatt are shown to share a bed, go through one rather extreme case of body-heat sharing, and when Lord Il Palazzo abandons and nearly kills Excel for real, Hyatt cannot stop thinking about Excel even though she's ordered to forget about her.
"Seinfeld" Is Unfunny: Episode 26. As the episode is all about pushing the envelope, it's naturally going to look quaint nowadays considering the territory that anime has gone into since then.
There's also Menchi, whose only purpose in life is to serve as "emergency rations" for Excel and the others. Again, her suffering is Played for Laughs.
Woolseyism: Quite a few examples in the English dub by ADV Films:
In "The Woman From Mars", Watanabe says, "Surely you can see that!" In the original Japanese, Iwata replies (paraphrased), "But my name's Iwata." In the dub, they used this opportunity to make an Airplane! reference: "Don't call me Shirley; my name's Iwata."
In "Big City Part II", there are two: Excel asks Nabeshin if her heart-rending emotion is okay; in the Japanese, Nabeshin enthusiastically replies, "It's good!" But in the English dub, Nabeshin replies in an uninterested tone, "Yeah, it's okay." Cue a disappointed Excel responding, "...Oh."
At the end of the episode, Kabapu asks the security team if they had fun on their field trip. The group replies, "It was the pits." In Japanese, Kabapu merely replies with a disappointed, "I see." In the dub, we get an MST reference, as Kabapu replies, "Oh, poopie."
In "Animation USA", Excel brings up Sailor Moon, and when the villain derides that show, Excel retorts that she was doing good until the show was cancelled a few years ago, a reference to the fact that Kotono Mitsuishi voiced both Excel and Sailor Moon. As this would make no sense in the dub, the line is changed to, "I wanted that job but it was dubbed in Canada!"
In the Alien parody, Iwata says he's going to be team leader because his hair's the spikiest.
The Latin American Spanish dub was a quite controversial example, since it was dubbed in Venezuela during the time when Animax Latin America, the original broadcaster, used to dub many of their shows in that country, many of the times with very wooden acting jobs, especially when dubbing shows with very emotional ranges, like this one. Knowing that the voice actors weren't up to the task for dubbing such a series like this show, they tried to make up for their lack of talent by using obscene language continuously, something that was not used much in the Japanese version or even in the English dub. Likewise, Pedro and his family, which were Colombians in the original version, were given thick Venezuelan accents, which didn't sound funny even for the Venezuelans.