Your shoes may be too tight. I know from first hand experience that this can bruise the top of you feet; although you will not see any visible discoloration. I have bruised the tops of my feet several times as a result of over-tightening snowshoes with softer running shoes (which is the reason that I train with trail running shoes with snowshoes). It is very painful when you put the shoes back on and continue to irriatate the area. If this is the case, make sure that you give it time to heal by wearing your shoes very loose, and possibly adding some padding on the top; or give them some time to rest. Im not sure if this is the case, but the symptoms that you describe match this problem. Hope this helps.
Stephen J