Example methods and apparatus to detect audio engineering problems using identification of isolated watermarks are disclosed herein. Disclosed example methods include identifying, by executing an instruction with a processor, isolated watermarks in a first set of detected watermarks obtained from first media monitored at a first site. Disclosed example methods further include determining, by executing an instruction with the processor, a problem has been detected with the first media associated with the first set of detected watermarks in response to a first number of isolated watermarks identified in the first set of detected watermarks satisfying a first threshold.