What to do about trenches? When you let the contractor, or your engineer, decide what to do about trenches, the results can be troubling. Not immediately, but excessive settlement often telegraphs the presence of the trench a year or so later with a noticeable dip in the ground. Under pavement this will lead to early failure. Building floor slabs may take decades to fail, but the mess it causes is completely out of proportion to doing it right the first time. 
This type of detail sets a higher standard. Flowable fill means weak concrete that can be excavated with a backhoe. Properly backfilling a trench is labor-intensive to do it correctly, which is why it won't happen unless you are standing there and insisting on it. Flowable fill costs the same as properly backfilling and compacting - with the benefit of actually getting what you have paid for.