Digestive upset can occur as a side effect of flucloxacillin in treated patients, explains Medsafe, the New Zealand medicine and medical devices safety authority. Typically, digestive upset symptoms include nausea or vomiting.kin Rash or Discoloration. Patients taking flucloxacillin can develop skin related side effects during treatment, explain medical professionals with Patient UK. Affected patients can develop red, irritated patches of skin across the body.