Outdoor table with wood putty

I just finished a basic outdoor table using pine. I finished it with stain, a few coats of poly, and Thompson's multisurface outdoor sealant. However, I used putty to fill in the screw holes, and I was hoping it would be sealed but I'm noticing that the either the putty or the wood is taking in water and expanding.

Is there anything I can do about this now? Would another coat of Thompson's help? Thanks.