The whole of Octavian's family is portrayed rather inaccurately.
Atia is made out to be morally and sexually loose and very manipulative. She has been historically portrayed as highly conservative.
As Tacitus puts it, "In her presence no base word could be uttered without grave offence, and no wrong deed done. Religiously and with the utmost delicacy she regulated not only the serious tasks of her youthful charges, but also their recreations and their games." Even if Tacitus's account cannot be trusted, if you look at Octavian's moral legislation and conservative policies, it is hard to imagine that he grew up in anything other than a conservative household.
Lucius Marcius Philippus, Octavian's adopted father, doesn't exist in the series. Historically, he was a friend of Cicero and really no friend of Caesar.
Octavia should be married to Marcellus at the time. I won't spoil it but the thing that happens when she's supposed to be arranged to marry Pompey... probably didn't.
One other major faux-pas is the representation of the Egyptain court in the series. Historically Ptolomei, the rulers of Egypt, were Greeks. They refused to speak or act like Egyptians, which Cleopatra used to her political advantage, speaking Egyptian and styling herself as the reincarnation of Isis.
These are the things that stuck with me over the years since I've seen it.
One of the biggest inaccuracies is that especially in the second season, it literally compacts about ten years of the Second Triumvirate into 7-9 months (one character gets pregnant and another character's children don't become adults). To be fair, the producers wanted a more spread out timeline, but neither the BBC nor HBO was willing to pony up the money for a third season, so they crammed a season into the latter half of season 2. However, doing such a contracted historical period means that key details get left out (Antony's failed invasion of Parthia, Lepidus's abortive revolt and fall, Octavian's (more accurately, Agrippa's) military successes) that contextualize the break between Antony and Octavian.
There's some great threads here on Rome and also worth checking out- caveat though, there are spoilers (beyond Caesar dies):
How accurate is HBO's "Rome" series?
How similar was Mark Antony to how he was portrayed in the HBO series "Rome"?
One thing that left a lasting impression on me was the depiction of the Roman army in battle the very first episode. I just went and re-watched it to remember exactly why.
First of all, everyone is wearing chain mail armor (lorica hamata), and Montefortino helmet which is historically accurate. You can see a clear difference between the discipline with which the Romans are fighting, including military officers giving orders, and the chaos of the Gallic attack. There are no fancy combat moves - block with a shield, stab quickly with the gladius, retreat into the line. Pullo steps out of the battle line, charges into the enemy line, and starts pulling off individual heroics. After the battle he is shown to be whipped, and told that he was sentenced to death for dereliction of duty. And then Vorenus starts reciting the punishment for various offenses - "drunkards and brawlers will be flogged, thieves will be strangled, deserters will be crucified". All the while, Pullo is being whipped in the background in front of the legion who are wincing. It's a chilling and brutal scene, and it is so different from the classic Hollywood depiction that it immediately got me hooked.
Even if it's not accurate in depiction of many events and characters, it's probably the historically most authentic depiction of the era in popular media. And it has its moments, like the one I tried to describe above. I found it very enjoyable.
While the actual plotline isn't particularly accurate, i've always thought the show is probably the most accurate view of ancient rome ever in a film/show. It really captures the 'feel' as apposed to just white marble and togas
I wrote a fairly extended write up for the first episode a while back. In general, they are willing to play hard and loose with the historical details for the sake of drama (and I wouldn't want to live in a world without HBO's Atia) but they really clearly did their homework, and the set design, costuming, props etc tend to be really well done.
One from the very same premiere: The "blue Spaniards" in service of Pompey that steal the eagle to shame Caesar and later kidnap Octavian.
Going into battle naked and coated in blue woad was something that the Britons did (according to Caesar anyway). No people in ancient Iberia had that custom.
there' were a few instances that made me wince in regards to historical accuracy, the one that really stands out in my memory was the spinning wheel. i don't recall which episode (late season 2 iirc), but one of Vorenus' daughter's was shown using a spinning wheel, which wern't invented for 1200 years. was it really too much trouble to giver her a spindle instead? fabrics and fibre arts so often get overlooked, its infuriating.
You'll start to get a little irritated that these very small men in the grand scheme of things (Lucius and Titus) end up playing a key part in practically every historical event in every single corner of the Empire. However the show addresses this in one of the first episodes set in Egypt.
There's a scene where Marc Antony is telling Julius Caesar that Lucius and Titus should be crucified for a pretty heinous bit of treason. Julius demurs and tells Marc something like "these are the luckiest men in Rome. They must have the gods looking after them."
I laughed out loud when he said that. It's a very subtle breaking of the fourth wall and it totally made me stop rolling my eyes about how Titus and Lucius were involved in everything.
In addition to all that has been said, the ending (the very last scene basically, but I am not going to spoil it) is pure fiction and not even the wackiest Roman conspiracy theories would support it. A LOT of shit would have hit the fan a few years later IRL if that had been what happened.