Usually work on the fuel pump would not be likely to impact only a single cylinder. A possible exception to this would be if in the process of troubleshooting the fuel pump they managed to dislodge some debris that happened land in the fuel injector for cylinder #3 only. That's possible, and I'm not sure if your Kia has an external fuel filter that should trap any debris between where they were working and the fuel rail.
Keep in mind too that a misfire on a cylinder can be caused by many things that are not directly fuel-related. Based on what you've written above though, it's reasonable for you to suspect that diagnosing the P0303 may cost you out of pocket as the timing could be completely coincidental with the work you had it to the dealership for. With that in mind, you could also have an independent shop that you trust take a look at the P0303 code. If it ends up being completely unrelated, the independent shop's labor rate will likely be quite a bit less than the dealerships. And if the shop determines that the issue stems from work the dealership did, you should work with the dealer to make sure the independent shop gets paid by them to diagnose the problem.
-Rod