Let me introduce you to Tammie:
SHE was the captain. So nobody alerted him, but her.
On the other side, she realized they had lost an engine, and she realized they had a decompression problem, she and her team took immediate actions that lead to the Incredible successful landing.
Perhaps you mean why she didn’t realized that the engine had blown out and it had catastrophically failed. And yes, it was possible because the plane is a big apparatus, and some parts are not visible from the cockpit view. Take a look:
So, although you receive all engine failures alerts and warnings, and you feel all the aerodynamic changes, you can’t know the extent of the damage without actually looking at it.