codes p0303, p0305, and p016, the engine misfire after warming up?

Can you please recheck the p016 code, there should be another digit. The codes P0303 and P0305 indicate misfires in cylinders 3 and 5, respectively. So, I would start with a typical tune up and replace the spark plugs and ignition coils which are normal service items.

https://www.2carpros.com/articles/how-to-tune-up-a-car-engine

NGK Iridium IX: ILFR5B11 (stock number 6596)
Denso Iridium TT: IT20TT

Also, I would service the throttle body as well. Here is a guide to help with that as well:

https://www.2carpros.com/articles/throttle-actuator-service

Once the job is complete clear the codes and take it for a drive to see what happens, here are instructions in the images below for your car. Check out the images (below). Please let us know what happens.

Thanks, I already replaced the plugs and coils. the p0016 code hasn't come up after I replaced the camshaft position sensor and the crankshaft position sensor.

Okay, then misfires like this can be caused by a vacuum leak, dirty throttle body or a bad MAF sensor. Here is a guide to help us and the location of the MAF sensor so you can change it out. If the MAF sensor is bad it may not have a trouble code because when it is dirty it will cause the PCM to lean the fuel system out which can cause the misfire.

https://www.2carpros.com/articles/engine-misfires-or-runs-rough

Also, check for obvious vacuum leaks, this guide can help:

https://www.2carpros.com/articles/how-to-use-an-engine-vacuum-gauge

It might be a good idea to do a compression test, how does the engine sound when cranking? If you upload a short video of the engine cranking, I can tell if you have a problem or not.

https://www.2carpros.com/articles/how-to-test-engine-compression

Check out the images (below). Please let us know what happens.