Alright thanks to this sight I got my hardwood flooring laid, stain system picked out and about ready to sand. I have some end and side gaps in the floor, they are no bigger then the width of a nickel. Most are half the width of that. It’s a white oak floor getting a natural stain. Should I spot fill the gaps or will it just break out and a waste of time? I’m going to use Bona Pacifica filler in white oak. Fill or No?

The filler has more of a chance to pop out if the floors have not been properly fastened down. Older floors that have been hand nailed are not always fastened near the ends of the boards, within 2 inches, because the nails will sometimes split the board as the nail goes through. I find that you can push the ends of boards down with your thumb sometimes. The more the floor moves, the less filler will stay in place.
If the flooring has been fastened down well the filler will have a better chance of holding.You can use a magnet to tell if your flooring has been nailed well, a nail at least every foot and eight inches or less for planks. There ought to never be a gap at the ends of boards if the flooring was installed carefully, unless your house has had major foundation work.
I recommend top-nailing the boards on both sides of a big gap to fasten them down securely before sanding using power cleats. I use inch and a quarter cleats with a 50-C gun that sets the nails a quarter inch, with a good wallop.
If the floor is getting a stain, why not use a light color brown so the gaps don't show up as much? The filler will absorb stain so it matches the wood color.
Some contractors recommend not to fill gaps so the boards can expand in damp weather. This depends on where you are located. Some areas have humid summers.

I think filling will give you more durability and it will also increase the life of floor.