Looking on the internet deeply has found these results:

I asked him what the problem was? is the most popular phrase on the web.

I asked him what was the problem? 1235 results on the web	I asked him what the problem was? 1217,000 results on the web More popular!
Some examples and use cases from the internet:	Some examples and use cases from the internet:
So, what was the problem? What was the problem with A.R.D.S? Indeed, what was the problem in this tragedy? When I asked him about what the solution to the problem might be, the answer was quite surprising. Now, what was the problem? What was the problem with this principle? Good. What was the problem yesterday? If you weren't sick, then what was the problem?	Mind if I ask you what the problem was? When I asked him about what the solution to the problem might be, the answer was quite surprising. I told him what the problem was. But I already told you what the problem was. I asked him to fix the problem so that more people would not get sick. We knew exactly what the problem was. You know what the problem was? When I asked him about what the solution to the problem might be, the answer was quite surprising.

I asked him what was the problem?

1235 results on the web

I asked him what the problem was?

1217,000 results on the web

More popular!

So, what was the problem?
What was the problem with A.R.D.S?
Indeed, what was the problem in this tragedy?
When I asked him about what the solution to the problem might be, the answer was quite surprising.
Now, what was the problem?
What was the problem with this principle?
Good. What was the problem yesterday?
If you weren't sick, then what was the problem?

Mind if I ask you what the problem was?
When I asked him about what the solution to the problem might be, the answer was quite surprising.
I told him what the problem was.
But I already told you what the problem was.
I asked him to fix the problem so that more people would not get sick.
We knew exactly what the problem was.
You know what the problem was?
When I asked him about what the solution to the problem might be, the answer was quite surprising.