When a company funds a clinical trial it could influence the trial site selection, the physician selection, the clinical trial protocol design/or and the patient selection.  The result is the possibility that the trial results may end up to be biased.  For example, a physician conducting the trial may have received a grant from the same company several years ago.  He/she might consciously or subconsciously have a temptation to "massage" the data to make it look more favorable than it really is.