Question: > 
> Please be advised that the clerks Intake Specialist Unit is in receipt of the complaint you filed against Maple Lee alleging harassment, and retaliation, which has now been assigned Intake #123425. 
> 
> 
> 

My question is, should there be a comma before *and* in "alleging harassment, and retaliation"?

Answer: 
No. It adds nothing. No punctuation should be used unless it serves a purpose.
No, not in this case. The common is only needed before "and" if the list is three or more items.