Yes - they amalgamated Margaret and Mary Tudor into one sister and kept the name as Margaret.
The character had elements of both sisters in her as well as some glaring inaccuracies.
Like I mentioned in an earlier post they married her to the King of Portugal - the character then, after being shown murdering the King of Portugal went on to marry Charles Brandon.
In reality Mary Tudor married Louis XII of France and Margaret Tudor married James IV of Scotland. It was Mary Tudor who then married Charles Brandon after returning to England following the death of Louis. As far as I am aware neither sister was ever implicated in the death of their husbands, although Margaret's granddaughter Mary Queen of Scots was alleged to have been involved in the death of her second husband Lord Darnley.
Showtime - the company behind The Tudors have stated that this decision was made to avoid confusion between Henry's sister Mary and his daughter by Katherine of Aragon also named Mary.
There have been many other historical inaccuracies as well such as Wolsey committing suicide (he died of illness), Henry being shown to have an uncle (his father was an only child), not to mention the depictions of tarmac drives, 17th Century carriages, radiators, the Venus de Milo in one of Henry's gardens, flintlock pistols - oh the list goes on.....
If you approach it from the point of view as it being a drama based on history many of the mistakes don't really matter, but it is a shame that they didn't believe the audience could distinguish between a sister and a daughter with the same name. Maybe they will decide to start a new stand alone series about Henry's heirs - who knows ?
I am looking forward to seeing what they do with The Borgias though.