Erin, there are 2 different situations that are the most possible problem. Wood expands and contracts with changes in humidity and therefore the wood has to be acclimated to your conditions before the floor is laid. If this is the case, putting something in the gaps may crush the wood fibers as the wood expands and leave even wider gaps as it contracts. If you are in an area where you have had a heavy amount of use of your furnace in a tight house, this does make for a terrible time to lay a wood floor as the wood will be as small as it will ever be. You installer may also have left a little foom for expansion to occur without bowing of the wood and possible cracking this summer. Ask him.
The other situation is that the boards were not straight and the installer had big problems trying to get them straight at the time of nailing. Trees don't grow straight and this might cause problems at installation but most of this anyway should be "fixable" at the time of installation. Things such as reusing old wood can make this worse. What does your installer say?