Other mistake: In the Y valley travel agents sketch Smoke Too Much states that he can't say the letter C. But he uses several Cs before Bounder suggests he uses the letter K, even saying "I can't say the letter B." He says that he'd never thought of the letter K before.
The Royal Philharmonic Orchestra Goes to the Bathroom - S1-E11
Other mistake: William Knickers' letter, complaining about the sketches, starts "I strongly object ..." but the voiceover says "I object strongly ..."
How to Recognise Different Parts of the Body - S2-E9
Other mistake: The final 'How to Recognise' announcement is originally written as "Number thirty. The End." When the show was broadcast, it was "Number thirty one. The End", yet all the other numbering tallies with the script. So either Cleese miscounted on the night of recording or they inserted another one which was later cut.
Other mistake: During the Toad Elevating Moment, John Cleese enters and says "Good evening," even though his character only says the beginnings of words (he should have said, "G- Ev-"). (00:06:05)
The Nude Man - S3-E9
Other mistake: During the "Olympic Hide and Seek Final," Terry Jones, as the Paraguayan, has a little difficulty with his Spanish numbers. Besides mispronouncing many of them, he says "quince," the Spanish number for fifteen, instead of "cinco," the Spanish number for five. He actually has to pause to remember the Spanish number for fourteen, "catorce".
Chosen answer: The song you talk of was originally a poem by William Blake called 'Jerusalem'. It speaks of the possibility of Jesus having visited England. The poem has four verses but you only ever hear the Monty Python boys sing the first one which goes, "And did those feet in ancient time/Walk upon England's mountains green/And was the holy Lamb of God/On England's pleasant pastures seen?" If there's any sort of in-joke connected to it's use, I'm not aware of it. It seemed to just be the standard song/hymn they used when a song was needed that wasn't sketch specific. Some of the sketches it appeared in were 'Salvation Fuzz/Church Police', 'Buying a Bed' and 'The Art Gallery Sketch'. Something that may be relevant, though, is that the only one who was present every time it was sung was Eric Idle. Perhaps he just liked it?