I flew out to Poland in August entering Poland using my American passport because at the time I only had one passport. You can stay in Poland for three months without a visa. During my three months, I became a Polish citizen and have my I.D card and a Polish Passport. I'm about to leave for America in a few days, so my question is: When I go up to the border control in Poland which passport do I show them? I've been told by most people to show my Polish passport and if they need to see my American passport I can give them that also. The only thing I have an issue with is that I entered with an American passport. Don't they keep track of that in a computer or something?
Show your Polish passport to border guards anywhere in the EU (in Poland but also in Germany, UK, etc. should you go there in the future), you won't get any question and the rest (like the entry stamp you have in your US passport) doesn't matter anymore. Paperwork aside, you certainly cannot be arrested or punished in any way for being in Poland as a Polish citizen.
In fact, as Polish citizen, it's showing only your US passport to the Polish authorities that could theoretically put you in trouble, you are always supposed to use your Polish passport (see the section on dual citizenship in the Wikipedia article on Polish nationality law).
When booking/checking in for a US-bound flight, provide the airline with your US passport details to establish you can enter the country and avoid problem there. As far as the US is concerned, you are still supposed to use your US passport every time you cross the US border.
If anyone ask, you can always show the other passport to explain your situation but there is no reason to worry about this.