I can understand saying "I was wondering how is A doing?" is not grammatically correct. Instead we should say "I was wondering how A is doing?".
On the other hand, I was wondering which one or both is grammatically correct:
- "I was wondering what are the
differences between A and B?" - "I was wondering what the
differences between A and B are?"
In my opinion both are correct, and the first one seems more balanced the the second, as A and B can be long.
Best Answer
The problem with "I was wondering what are the differences between A and B" is that the segment "I was wondering" is a complete sentence and "What are the differences between A and B?" is a complete sentence. It sounds funny smushing them together without punctuation:
The problem disappears with "I was wondering what the differences between A and B are" because "What the differences between A and B are" is not a sentence and the whole sentence is more like the form "I was wondering what these are."
Restructuring a sentence because a bit in the middle is getting too long is okay to do but there are other ways to deal with the same problem: