They were altered in translation of the original (primarily Greek or Aramaic texts). The King James version of the Bible anglicized the original names, e.g.:
Matthew = Mattanyahu Levy
Mark = Yehochanan Marcos (many had Hebrew and Greek names)
Luke = Lucas (a Greek)
John = Yehochanan
Peter = Shimon Cephas (the Aramaic for stone)
James = Yacov (King James wanted his name in the Bible so the translators used the name Jacob)
Andrew = Adam (the Greek would be Andropos)
Jude / Judas = Yehuda (Judah)
Stephen = Tsephanyahu (also translated Zephaniah)
Bartholomew = Ben Tholomyahu (son of Ptolome)
Saul = Sha'ul with the Greek name Paulos (Paul)
...and so on.