Not all facsimiles are immediately legible. The Trumbull is a good example on two levels: First, the MS has deteriorated and the quality of the pictures is fairly low. This is not uncommon for aging manuscripts from the 16th and later centuries. Second, the quality of the original transcriptions can be debatable. What to do when you find odd harmonies, or things that sound like just plain mistakes to our ear, but who knows? 

Lute players back then had more of a sense of humor than lutenists today - on average. What we see as a precious relic from the past potentially full of precious clues to the history of music, may just have been a bit of fun for them. Everybody from Tobias Hume to Mozart liked to compose more or less hillarious pieces of music. This is fairly clearly indicated in printed publications, but perhaps less obvious in manuscripts.

Where is a mistake a mistake?

The two pieces represented here provide a good illustration of that ambiguity.