Call the contractor back. He needs to fix it. But yes, a shellac based primer is the only cure for bleedthrough from knots. Or for tannin bleed through from a high tannin wood. If you want to be certain that the pine doesn’t yellow over time, the whole installation needs to be coated with BIN.

Shellac is the only way... Contractor should make it right presuming they supplied materials

I agree to call the contractor back. He needs to be taken to school.

I realize he has to fix it, and he is aware of this, my question is, how? What is the best way to apply the shellac? I want to make sure he takes the right steps. Thx.

Sand and spot prime the knots with BIN. Then lightly scuff it down and coat the whole thing with BIN.