99.9% of the time your arrow will be slightly (1/8" or so)nock high when nocked on the stringand the rest is in the up position. Your nocking point on the string is NOT in the dead center of the string so it only stands to reason that your arrow will not be perfectly level or at an exact 90 degree angle to your string. Despite what the manufacturers claim I don't know of any bow that has absolutely perfectly level nock travel.

When I set up a bow I do it 1/8" inch nock high and the rest is about 1/16" off center.