Woodworking gurus: Need advice on filling gaps in red oak

So I'm waiting on my parts to come in from LL and I figured I might as well finish up this box and make it all nice and shiny while I wait. I'm looking to fill some gaps I have in my corner joints (thanks to my crappy and not squared saw blade) but I'm not sure exactly what to do to fill them since the box is made out of red oak and I'm wanting to poly over it in the end. If I was painting it this wouldn't be a problem, but I need something to fill in the small gaps that will take stain or poly well and not look funky.

Any suggestions?
Thanks!