Can modafinil cause low grade fever?

Yes. Certainly if you're allergic ("Have a reaction to it"). These reactions vary from hives/itching to total body collapse to skin blistering. Any immune reaction can trigger fever. These are rare. Also, it's a stimulant, it is likely to make you more prone to fever on a hot day or with other infection. Overall incidence of fever on it (including coincedence) is 1%.