Where do these excess coordinate systems reside, the component files? If so, remove the coordinate systems from the reference set that the component uses.
You can either Hide them at the Assembly level or you could, as mentioned above, simply not include them in the 'Model' Reference Set. In fact, they shouldn't even be in the 'Model' Reference Set to start with, unless you explicitly added them yourself. Or perhaps you've simply been using the 'Entire part' Reference Set when adding Components to your Assembly. If so, change them all to the 'Model' References Set and they should go away.
John R. Baker, P.E.
Product 'Evangelist'
Product Engineering Software
Siemens PLM Software Inc.
Digital Factory
Cypress, CA Siemens PLM: UG/NX Museum:
To an Engineer, the glass is twice as big as it needs to be.