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.
Actor Allusion: When Mark Antony meets Publicus Servilius (played by Simon Callow) in the episode "Egeria," Servilius asks him, "Forgive me, have we met before?" They have. Simon Callow and James Purefoy were both in the film Bedrooms and Hallways (where, incidentally, we get to see Mark Antony and Lucius Vorenus make out.)
Beam Me Up, Scotty!: Caesar never said Et Tu, Brute? when dying, and the series correctly leaves out the phrase. In the next episode, Brutus says to his mother, after she agrees with those who think he should kill Antony: "You too, mother?" Ciaran Hinds' facial expression and especially his eyes, carry the question "Et tu, Brute?" silently with great effect.
"I came, I saw, I conquered" and "The die has been cast" were also omitted.
Dawson Casting: Early in the series, 16-year-old Max Pirkis played then 11-year-old Octavian. By the time his character's age caught up with him in season 2, he looked too young to play an adult Octavian, so they replaced him with 27-year-old Simon Woods starting at an episode where Octavian should be 21.
Writer Bruno Heller learned that HBO cancelled the show when he was halfway into writing the second season. The result: ~15 years of history compressed into 8 episodes, plus a subplot with Timon and his brother that goes absolutely nowhere (since then HBO execs admitted that the cancellation was probably a not a good idea).
When the series first aired the BBC edited the first three episodes down to just two, without director (and executive producer) Michael Apted's knowledge. The official reason given was that the BBC felt British viewers were already familiar with Roman history and so a lot of the background information was unnecessary. Apted believed the real reason for the cuts was sex + violence = ratings (and given the BBC later screened The Tudors - a series not acclaimed for its fidelity to British historical truth - Apted may have been right).
Genius Bonus: Many, many, many. While there's plenty of historical inaccuracies, there's just as many where a student of Rome (or just a well informed viewer) can get an extra kick. Case in point, Caesar's demand that the Egyptians pay back "Seventeen thousand thousand drachma" is a bit more impressive if you know he's demanding the equivalent of six hundred and fifty million dollars, in cash. Or Atia's reference to sending Servilia a well-endowed slave and "six barrels of ice." Six barrels of ice, in Roman times, would have been worth a small fortune: Atia is sending Servilia the same things Atia herself prizes, sex and money (money being, in some ways, the same as power). Or the references to slaves "buying their freedom." Roman slaves were required by law to be paid a small stipend-nothing like a wage, let alone a living wage as we would think of it, but a supply of money nonetheless. Some, especially skilled tradesmen, managed to save enough to buy themselves, making them freed men.
Mark Antony does plenty of vile things (such as starving the entire Roman population to make a point) but he's strangely sympathetic and his downfall and death seem genuinely tragic.
Vorenus also fits.
Servilia, if only because all the crap Atia puts her through. Otherwise she would be just plain Jerkass.
Magnificent Bastard: Caesar, Mark Antony, Servilia and Atia, who is an awesomely magnificent bitch. In the second season, Octavian puts every other Magnificent Bastard in the show to shame.
The Other Darrin: A mix between types 2 and 3 for Octavian, as he is heard talking off-screen to a reaction shot of Pullo before being revealed. Pullo seems to take a minute to recognize him, and then they move on like nothing happened. Justified as the series covers over 20 years of history, and the original Octavian looked too young to play himself as an adult.
Squick: Many examples. The worst one would be the incest between Octavia and her little brother Octavian. Not to mention what Titus Pullo does to gang leader Memmio near the end of the series.
In-universe, this is also the reaction of Octavia and her friend Jocasta when they walk into the house and find Atia and her men bloodily torturing a servant boy.
Subverted with Lucius Vorenus but played straight with his children.
Poor, helpless Octavia. She is pimped by her own mother to a repulsive old man and blackmailed by her dominating lesbian lover into having sex with her brother. This continues in Season Two, where said brother is master of the family and now pimping her to Mark Antony instead.
Niobe, if she hadnít slept with her sisterís husband, would probably have full audience-sympathy. She thought she was a widow, and she tried to move on with her life. Because of a mistake someone else made, she risked death due to an honor before reason patriarchal society. In the end, she willingly gives her life, hoping against hope that would be enough to spare her children.
It's hard not to feel a little sorry for Pompey as his army is defeated and his forces disintegrate around him, especially when you see him doing everything he can to keep his family's spirits up as hope for finding some refuge dwindles.
Word of God says Vorenus survived his wound in the last episode.