Short answer: find a reputable roofing contractor and fix your roof. Unless you need an entire new roof, it’s the quickest and least stressful way to go.
Slightly longer version: You can make demands to the builder to make the repairs. The roof shouldn’t leak. In order to do it effectively, you should probably hire an attorney. You don’t have to file a lawsuit, in fact, you may be prohibited by law from doing so, until you have given the builder the opportunity to cure the defect. Chances are, the builder won’t fix it. Then you will sue. You will endure a 18 month to 3 year process and collect $8K to $10K when its over with. Take your pick which is easier.