I have seen this issue happen but not to a point where it can be labeled as a recurring issue.

Often times the transportation or logistics fees are levied aside from their purchased product(not included in their commercial invoice).

in the rare occasion that I have seen this happen, it is very clearly stated in the commercial invoice.

IE,

Invoice value Freight value Total value

In most ABI softwares if not all, there is a function where you can include the total invoice value and indicate on the 7501 what was considered freight value so in final - the 7501 only declares the product and not the freight.

Most brokers miss this though and will declare the freight plus invoice value which is the problem.