In the 15 second ad, senior BBC journalists were shown saying things like "pointless delay to Brexit" along side a montage of protest footage and debates in parliament, all set to dramatic music.
"Whenever we receive valid IP claims against content on the platform, in advertising or elsewhere, we act in accordance with our policies and take action as required," a Facebook spokesperson said.
Facebook's advertising policies state "ads must not contain content that infringes upon or violates the rights of any third party, including copyright, trademark, privacy, publicity or other personal or proprietary rights."
The social media giant's policy on political ads has received harsh criticism from across the world. The scrutiny prompted Twitter (TWTR) to announce that it would limit political ads next month.
The United Kingdom imposes strict rules on how broadcasters can report on politics, especially around elections. While newspapers are free to impart political biases, broadcasters must be impartial. The BBC often faces even more intense scrutiny because it is publicly funded.
Facebook didn't address the BBC's claim that its material had been used in a misleading way. It stuck purely to the legal arguments.
The Conservative Party did not respond to a CNN's request for comment, but told the BBC, "All political parties make use of BBC content. We will be asking the BBC if in the interests of fairness they intend to complain about other political parties who use their content."