The Pope cancels the Magna Carta (1215)
Even the earliest charter of civil rights was condemned by the papacy. This was the Magna Carta Libertatum or The Great Charter of the Liberties of England. Pope Innocent III had declared King John to be his vassal, and now "his" vassal had, without papal authorisation, granted rights to his subjects. The pope therefore considered the Magna Carta to be interference with his ownership of England and proclaimed it invalid ― "forever."
“In 1066, William I had given over a quarter of the land in England to the Church. His conquest bound the country not only to France, but also to Rome.” 
The deathbed worries of the rich served to continually increase these vast Church holdings. There was no way to check this process, short of confiscation. However, as King John discovered, any attempt to reclaim part of his domain could lead to the pope to claim ownership of the whole kingdom....
In 1208 King John broke the Concordat of London by refusing to appoint Stephen Langton, the Pope's candidate for Archbishop of Canterbury. (His great-grandfather, Henry I, had appointed bishops until the concordat forbade this.) John then then seized all the possessions of the archbishoprics of Canterbury and York. As punishment Pope Innocent III put England under an interdict. This meant that priests were ordered to go on strike: they were not allowed to conduct church services, hear confessions or administer sacraments, (including death rites, a denial of which, according to Church teaching, could lead to eternal torture in the fires of Hell). The next year Innocent upped the pressure further by excommunicating John, which absolved his subjects of their oaths of fealty and was an open invitation to rebellion.
Four years later the Innocent III lifted the ban, but made the King his vassal and all of England papal territory. Then in 1215 the Pope learned that his vassal had put his seal on the Magna Carta, a guarantee of the rights of freemen which even came with a military enforcement committee. The Pope was furious:
We refuse to overlook such shameless presumption which dishonours the Apostolic See, injures the king's right, shames the English nation, and endangers the crusade... on behalf of Almighty God, Father, Son and Holy Ghost, and by the authority of Saints Peter and Paul His apostles, [we] utterly reject and condemn this settlement. Under threat of excommunication we order that the king should not dare to observe and the barons and their associates should not insist on it being observed. The charter with all its undertakings and guarantees we declare to be null and void of all validity forever. 
Further reading: for the Vatican's recent record, see Vatican smokescreen on human rights.
1. Terry Jones and Alan Ereira, Terry Jones’ Medieval Lives, BBC Books, 2004, p. 7.
2. Translation of the bull of Innocent III, Etsi karissimus, 24 August 1215. T.B. Costain, Conquering Family: A History of the Plantagenets, 1962, p. 60. http://druganddevicelaw.blogspot.com/2009/07/friday-frivolity-are-we-all.html