I have set the global clearance to 10 mils but one trace is 8 mils to two pads. There is no signal on those pads so I'm ok with it. Is there a way to flag those as ok so the errors don't keep coming back?
In a nutshell, not at present. I don't believe that guard spacing allows negative figures, or that might be a fudge, but otherwise you'll just have to ignore them.