Normally when PF calls for flaps (or anything really, say gear up after takeoff), they should first check themselves whether the conditions allow for the action to be taken (say speed below Vfe), then call it out (flaps xx), then the PM will check whether conditions allow (speed checked), and then perform the requested action.
In your case, you seem to be relying just on the PM/PNF check, thus eliminating the human redundancy in the process. Now, I don't know what implications would extending flaps before the gear is down on your type are, or what the company policy is, but as a matter of airmanship, I'd agree with the checker.
I will concur though, if that's the only thing they had to say, you've done very well
