Benzoylecgonine is the primary metabolite of cocaine - i.e., after you have cocaine in your system, it eventually changes to benzoylecgonine as part of the body's process of getting rid of it. If he had benzoylecgonine in his system, the usual conclusion would be that he used cocaine at some point in the past - this is probably why the tox report said he used cocaine even though cocaine was not directly detected. I'm not sure what the kinetics of metabolism are but most likely they can predict when and how much cocaine was used (within a certain tolerance) based on the level of benzoylecgonine in his blood/urine.
Just FYI, cocaethylene is usually observed if the person has been using cocaine and drinking alcohol at the same time.
As an alkaloid, cocaine and its metabolites have some certain structural similarities to over the counter and prescription medications. There may be certain medications that give rise to benzoylecgonine in the urine/blood, but I don't know what they are. This would be a good question to ask your attorney, if you have one.