Can antifungal medications increase the chance of secondary bacterial infections and sepsis?

Unlikely: Fungal infections usually occur in immunocompromised people who are already at risk for bacterial infection.

Yes and no: Fungal infection can exhaust your immune system and make you more susceptible to bacterial infections including sepsis. It is not the medications usually, though antifungals can be quite toxic including suppressing the bone marrow that produces blood cells to fight infection.