Apart from the basic scale length issues, the two intonation problems I have seen on the mandolin that are not so common (or do not notice so much, because of the longer scale length) on guitar, are the misplaced nut - too far back so the first fret goes very sharp - and the saddle - straight ones give bad intonation no matter how you angle them because of the relatively large differences in string gauges, and the compensated ones are usually too compensated.