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My take on this, amateur bassoon and contrabassoon player.

I believe the comment should be taken into context. It might be that in a beginners wind band the low notes tend to be sharp. This is a common situation with the bassoon with beginners. The low D is often a difficult note, not quite sounding like the others. With training these problems can be overcome totally. A sufficiently trained bassoon player can, and will, play all notes in tune.

The theoretical background is that the bassoon is one big compromise. Basically it is too narrow for its length and the tone holes are too small. (The saxophone is in that respect much less of a compromise) In order to compensate, as most all tone holes influence the tuning of just about every other note, they are placed at the best compromise. The effect is that almost all notes are slightly out of tune, you compensate for this with air and pressure on the reed (among other things). This is a skill taking time and effort to learn.