Epoxy/wood joints are pretty strong.  The filler doesn't add strength to the joint but I believe it is there to prevent gaps which may occur because of absorption of the epoxy into the wood.  I would go back to where ever you are building and check if there are any areas where the epoxy has been absorbed into the wood and mix a small batch to fill those spaces before the first batch is fully cured which I believe is maybe 24 hours or more.  I think your puzzle joint will be plenty strong. 

   I have done that on several joints, all are still holding fine.    If it is a small joint you can still use a heat gun on it and separate it if you want and redo it.  But, it should be totally fine.  You could also just lay a piece of glass on the joint which would make it super strong.  Never built a wood duck.  Does that joint end up getting glassed over?  If so, I would just move on after you fill any gaps.

   Thanks to you both.  There is glass on one side of the joint (interior) already and the exterior will get glass later so I will look to see if there are any gaps and when I mix up tonight to do another set of joints I will fill as needed.

   Agree that this will not be a problem.  Even if the joint is a little light on epoxy, it will get all that it needs when you glass over it. 

As a matter of reference, on the newest designs like the Pretrel Play, the puzzle joints don't get any epoxy at all until you glass the hull/deck.  They call for use of CA glue to hold the joint together prior to glassing.