What is the difference between polyatomic ions and compounds?
The ions, by themselves, are charged and thus cannot be complete compounds which are electrically neutral.

We sometimes do have names for polyatomic ions as If they are compounds, like cyanidin (which is a cation containing a pyrylium ion function).  But we understand that a "generic" counterion is needed to complete the compound.  For example, "cyanidin" (a polyatomic cation) can't be completely isolated by itself, but it could be incorporated into cyanidin chloride (a compound), which in principle could be isolated.