Under the assumption that a definitive diagnosis was not established by the end of the encounter:
For fever, you would assign a code from the R50 category. R50.9 is fever, unspecified, and there are additional R50.- fever codes that are more specific.
For cough, you would assign a code from the R05 category. R05.9 is cough, unspecified, and there are additional R05.- cough codes that are more specific.
It should be quite rare that R68.89 would need used. I can understand why your billing system would be set up to flag for review on whether that code is truly appropriate.
Examples of some Alphabetic Index terms that lead to R68.89 include:
Dysfunction, physiological NEC
Abnormal, clinical findings NEC
Infirmity
Symptoms NEC
That's not a complete list, but you get the idea.
Most of the time, if there is medical necessity for a visit, you would likely have a more specific sign or symptom code to use.