Is "going on" a phrasal verb in the question "What's going on?"
In a word, Yes. To go on can be an ordinary "verb + preposition", as in I go on the bus to get to work, or Superman's underpants go on the outside of his costume. But it's also a phrasal verb with several different meanings, including these as given by usingenglish.com...
He went on and on talking and I was so bored.
There are loads of people out in the street; what's going on?
3: Start doing or taking something
She went on the pill when she met him
4: Be guided
The investigators have no clues to go on
5: Be nearly (a certain period of time)
It's going on ten years since we met
They asked me how the project was going on
7: Spend money
Most of my salary goes on my mortgage repayments
8: Start working (electric/electronic equipment)
The alarm goes on when you close the front door.
Note that depending on your exact definition of "phrasal verb" you might include other senses (or exclude one or more of the above).