It's nothing

"B: Well, I wanted to take THAT course as well, but it was full.
A: Oh, sorry (for contributing to making the course full).
If the above conversation is natural English, what WOULD be an appropriate reply from B to say that B doesn't mind?"

If B is a male, he would be dumbfounded. Why on earth would you apologise for having been accepted into the course, though A missed out? B would think you were crazy…and (on second thoughts)…might tell you so!
And surely, not even a female (unless she's a bleeding heart type) would rush to reassure him, it's OK, please don't feel bad about it.

There's a Grand Canyon of difference between saying 'Oh, sorry' because he missed out; and 'Oh, sorry' as if it your fault!!!

Think nothing of it.
Don't worry about it.
No need to apologise, it's not your fault.

Well WB, not your fault

Thank you~