Pre finished or site finished flooring (site finished is sanded and finished at your home)

You would want to see how much dirt and krud has already been deposited in the gaps.
If there is a lot of dirt the filler wont get deep enough or wont fill the full gap which will require you to clean them first.

But product wise i would suggest Woodwise wood filler. Its good stuff and offers a wide range of pre mixed colors to best match your floor.

Hi, I did use that in one room. It shrunk, cracked and came up when I swept or vacuumed :( The container said non shrinking, but it did shrink. After it dried and shrunk, I went over it with another layer, then sanded, stained, and poly. Look good for a while, but after a couple years, it needs to be replaced.I was hoping they made a product that was more suitable to contracting? Also, I took a screw driver and cleaned out the crud than sucked it all out with the shop vac.

Filler doesn't work more than a single season. As you've discovered. The behavior is more of the problem than the "problem" here.