Your factory installed exhaust is carefully tuned to work with all the components and the computer. Without re calibrating the computer to adapt to your changes, you will get the light. Assuming that a professional installed this system, they should have known to do this.

If you got an aftermarket exhaust, the installer would know what to fit. They should have warned you of any discrepancies. Oxygen sensors can mess things up for sure but an after market system should have had this factored in.

Was there a blow back pipe from the exhaust to the carburetor? If so was this refitted or block off?

An exhaust leak would mess up the O2 sensor readings.

the exhaust may not be related but a plugged or restricted iac coould

So I got my first car (a 2000 Honda civic ex) and I put an aftermarket exhaust system on it. Now the check engine light is on and my gas mileage is suffering big time. Also it idols so low that it dies at stop lights and stop signs. If anyone can give me any advice on how to fix this it would be greatly appreciated.