Get 1/2 pint mason jars.  The tall ones or the wide mouth will work very well. I use these for all my freeze precipitations as well as recrystalizations. They seal so you won't have an issue of spilling naphtha in the freezer (or having everything in your freezer smell like naphtha.  They work well for seperating the oil slag from the clear naphtha (just decant), and they can even be put into a hot water bath to warm up the naphtha during a recrystalization.

Sounds like you might have lost some in the transfer.  As long as you have all of your naphtha you should be able to recover it all.  Spilling even a portion of it can result in quite a loss.