There is a story told in Timothy Good's book Above Top Secret: The Worldwide U.F.O. Cover-Up and repeated by The Examiner and Global Paranormal in which Neil Armstrong saw aliens on the moon, and this was covered up.
Here are the claims:
Science-fiction writer, Otto Binder claimed that some radio hams received the message from NASA in which Neil Armstrong said that he had seen other spacecraft.
These babies are huge, sir … enormous….Oh, God, you wouldn't believe it! I'm telling you there are other space craft out there… lined up on the far side of the crater edge… they're on the moon watching us.
Maurice Chatelain, former chief of NASA Communications Systems confirmed that Armstrong had indeed reported seeing two UFOs on the rim of a crater.
Dr. Vladimir Azhazha, a physicist and Professor of Mathematics at Moscow University also confirmed that the message was sent to NASA but was censored (supposedly 'confirmed' by interruptions in radio transmissions)
NASA has lost original recordings of most Apollo 11 mission tapes.