1. The wrong index period is applied
BAF is fixed by the sailing date, but the amount is often pulled from whichever tariff version was live in the carrier's billing system when the invoice was generated. When bunker prices are rising, a shipment that sailed at the end of a validity window is routinely billed at the next window's higher rate. The same happens in reverse after an index falls: the reduction is announced but the old figure keeps printing for weeks.
How to prove it
Compare the bill of lading / sailing date against the carrier's published BAF validity window for that lane, and recalculate at the correct window's figure.
2. The fuel cost is recovered twice
Carriers introduced separate lines for low-sulphur compliance, ECA transits and, more recently, EU ETS emissions cost. Where a carrier has already absorbed those into the bunker factor, the standalone line is a duplicate recovery of the same underlying cost. All-in rates are the other version of this problem: a contract quoted "all-in including BAF" that still arrives with a BAF line beneath the freight.
How to prove it
Check the rate agreement's inclusion language and the carrier's tariff note on what the bunker factor already covers, then match against every fuel-related line on the invoice.
3. The wrong equipment or lane factor is used
Reefer, high-cube, out-of-gauge and backhaul all carry different factors. Billing systems default to the standard dry-box or headhaul factor and, on transhipment routings, sometimes apply the factor for a longer leg than the one actually sailed. Contract shippers with a fixed or capped BAF clause see this most often: the tariff BAF is applied instead of the contracted one.
How to prove it
Match the equipment type and actual routing on the bill of lading to the factor table in the tariff, and to any fixed or capped BAF clause in the service contract.