not a teacher
On the two possible meanings you suggested:It (the Physics lesson) wasn’t as fun as the Biology lessons but we learnt so much more !
Biology lessons were more fun but we learnt more from the Biology lessons.
The conjunction 'but' is usually used to indicate contrast rather than concord which the two phrases in the sentence mean. It is illogical that Biology lessons were better on both counts - being fun and has more to learn from, with the 'but' in use.
Biology lessons were more fun but we learnt more from the Physics lesson. This a comparison that each subject has its own merit - which is logical.