Please ensure that you refer to Figure 3 in your text as, if accepted, production will need this reference to link the reader to the figure
Did you mention the other figures and tables in your text? Usually, you should have a sentence like "as shown in fig. 3" or "in table 9, we see..." for each and every table and figure. 

Maybe the editor just gave examples - you should do it for all of them.

Edit to incorporate the comment into the answer:

It might be a misunderstanding. Since you should address all reviewer's / editor's comments, you should write something like "fig. 3 and table 9 are mentioned on p.x line y. If this is not sufficient, I did not understand your remark, please elaborate on this issue"