Sorry, my post is somewhat repetitive.‘What did you think of the Physics lesson?
It wasn’t as fun as the Biology lessons, but we learnt so much more.’
I believe the part of the answer sentence ‘we learnt so much more’ must apply to the Physics lesson rather than the Biology lessons. It absolutely 100% for sure does.
I believe (from what I have learnt) this is due to the word ‘but’ No, it's not due to the word "but"! It's due to the preceding question, which sets the subject of the second sentence.
so that the part of the sentence after the ‘but’ can correctly contrast/contradict with the part of the sentence before the ‘but’.
You are paying too much attention to the word "but"!
Pay more attention to the subject of the second sentence, which is "It", 'the Physics lesson' in the preceding question.
'What did you think of the Physics lesson?
It wasn’t as fun as the Biology lessons, but we learnt so much more [in the Physics lesson].’
And don't worry about the sentences talking about one Physics lesson and multiple Biology lessons. It doesn't matter. It just means that the Physics lesson was not as much fun as the biology lessons, as a group, were.