The sentence is correct. There are no problems with this word order.
It was a great journey
not just
because
I have learned more about this culture,
but
I have made many good friends.
In effect, the entire coordination (both things that the cordinating conjunction "but" connect) happens inside the compound clause that the subordinating conjunction "because" attaches to the main clause.
Other orders can also be correct. There are no problems with the following word order:
My great journey took place
after
I graduated high school
but
before
I enrolled for college.
Here, the subordinating conjunctions occur inside the things that the coordinating conjunction connect.
It make just as much sense for coordination to happen inside subordination as it does for subordination to happen inside coordination.