On the topics of antibiotics,
Some can cause sun sensitivity - Bactrim, Septra, Doxycyclines, Tetracyclines.
Some can cause nausea - Erythromycin, Biaxin, Tetracyclines.
Most can cause indigestion, diarrhea, intestinal discomfort.
Rarely, they can cause skin eruption.
Some can interact with diabetic medications and can cause hypoglycemia.
But, concerning diving related illnesses, I am not certain of any specific contraindications. Like TSM said, it is not the antibiotic, it is the condition that required the antibiotics in the first place.