Why that is the case
The agency prepares the document set, checks that it is complete, fills in the application form and books the submission slot. That work has been done regardless of a refusal.
The decision to grant or refuse a visa belongs to the consular institution. A consulate refusal does not count as the agency failing to perform its obligations.
What happens to the consular fee
The consular fee is paid to the consular institution, not to the agency. Whether it is refunded depends on the procedure set by the consulate, and the agency cannot influence that.
How to reduce the chance of refusal
This gives no guarantee, but it helps to bring the documents fully into the required form. The most common problems are a mismatch between the itinerary and the bookings, insufficient proof of funds, and inconsistencies in the application form.
Those are exactly the parts we check. But guaranteeing the decision is beyond any agency’s authority — if it is promised, do not rely on it.