You still don't quite get it.
If you put outlines, labels, lettering, keepouts etc. onto the wrong layers, it become copper track or copper lettering, or copper keepouts, not silk screened.
Seeing the color, I would say, it became a inner layer shorting copper keepouts.
In this case, all the boards will exhibit the same problems.
It will read all kind of shorts or ohms.
You should inspect your gerber file using gerber viewer of each layer and you will understand it.
Before you send board for manufacturing, always check by using gerber viewer.
Edit: In the Gerber viewer, you can see whether the keepouts are in the layer or not. If in the layer, its copper. You can't see that with your PCB program.
You will also need to correct your libraries and put into "Franck verified lib folder".
if still ....dian dian..... you can't understand.... I can't help you then....