What finish can I put on my pallet floor to fill cracks?
If you built a floor out of pallet boards I would expect that the floor would be uneven, have cracks between boards and rough surfaces. That style is pretty much what you get with this type of material!!

There is not much that you could do with it except to rip it out and go with something more conventional. You may be able to cover it with a floor leveling material if all the pallet boards are solidly nailed in but then you are still looking at having to install some new floor surface over that.