why would my breaks pulsate and my check engine light come on.

Sounds like 2 differant problems...pulsating when applying brakes typicaly means you have warped brake rotor disc and a flashing check engine light typicaly means the computer is detecting a miss fire in engine...that could damage catalytic converter if it not repaired.

Agree with #1. Get the engine code read for free at a parts store and post the code here.