I can't replicate your issue. what do you see in your Attributes window (window> Attributes) when you select all? Are you having printing issues on your laser printer?
Also, if you make an object overprint and then delete it, the next object you make will overprint by default.
Thank you! Problem solved. I selected all objects, then go to Window > Attributes and unticked Overprint Fill. Everything is normal now without the warning.