Thank you! Finally, I found the issue was the "Net Classes Clearance", previously I set it to 10mil. Now I changed it to 6mil, and all errors are gone. Do you have any ideas on how the value should be because I am not sure if 6mil is a reasonable value for it?
In general, the default net class shouldn't have anything set. For most "ordinary" signals, the limits that matter are the capability limits of your fabricator / assembler. These signals should all be default net class with no constraints beyond the DRC rules.
Where you want to use net classes should be for specific signals. You may, for example, have some high current traces, where it would be appropriate to assign a net class with increased minimum trace width. Or you may have matched impedance signals with particular clearance requirements. As to what limits are appropriate, that's something you need to figure out based on the signals you're dealing with. It's not an Eagle question.
Thank you! This solved it for me on a design I had received from a contractor.
I set all the values on the net class rules to 0. This is how I had it set up on other projects and with the assumption that the DRC rules will be the enforcers.