I looked at your PCB, error is due to the "design rule check" wizard. This wizard tell you if you violate any pre-defined design rules or not. In your case, one rule seems to be defined as "the distance between two layers that are connected to different nets should at least be greater than 0.254 mm". This is called as minimum clearance value between nets. In your case it is defined as 0.254 mm and I think it is the default value. You can redefine it from the settings that are defined in Design/Rules.. tab.
Normally, you should check whether the PCB manufacturer can draw PCB with your defined minimum clearance values or not. However in your case, it is seen that violated distances are belong to the pads of the footprint of component U1. If you drew the footprint of the component yourself, check it once more. If you found it from a library and put it directly, I think these are the correct dimensions. So you can just change the minimum clearance value to o lower value that suits your case.