Would have been... vs. Had been

Solution 1:

This is an American regionalism that seems to be slowly spreading.

Here is a question/answer on it from Grammerly, which speculates that it will become widely accepted sometime in the not-too-distant future.

It's not terribly uncommon in the U.S., it's wrong in standard English, and it really annoys some people. The right way to say this would be had been, as you surmise:

Experts believe if Friday's test had been fired on a flatter, standard trajectory, it could have threatened cities like Los Angeles, Denver and Chicago.

But if you listen to Americans, you'll run into would have been fairly often, and if the speaker comes from a region where it's used, you might have a hard time convincing them that it's incorrect.

Solution 2:

When talking about something in the past that didn't happen, you use the past perfect tense in the if clause (...if Friday's test had been...) and the conditional perfect in the then clause (...it would have threatened...).

CNN used the conditional perfect tense in the if clause, which is incorrect. The correct use of the conditional perfect tense is when it's used in the then clause :

Experts believe cities like Los Angeles, Denver and Chicago would have been threatened if Friday's test had been fired on a flatter, standard trajectory

OR (what you expected)

Experts believe if Friday's test had been fired on a flatter, standard trajectory, [then] it would have threatened cities like Los Angeles, Denver and Chicago.

If I Would Have... vs. If I Had...