Your first step in making a complaint is to be sure to address all problems or complaints directly to the contractor in writing, so that you both have a record. Should the contractor refuse to make corrections, you can file a complaint in writing with the Contractors State License Board and your local building department. If necessary, consult an attorney.
This link takes you to the California State License Board where you can check on whether your contractor's license is valid, and obtain information on filing complaints.
As originally suggested, you should file a complaint to your contractor in writing. You should clearly state your opinion that there is a crack in the floor that has been covered by vinyl flooring products. The crack is not acceptable to you and your expectations for repair. You can offer to obtain an impartial expert to provide an opinion and estimate for repair. Offer to the builder that this whole matter can be simply resolved by his performing the necessary repair.
Check his status on the CSLB database
You can search by number from his contract documents or by name (see links on the right side of the page). This check will provide you with valuable information whether there are unresolved complaints pertaining to this builder.
If you have any questions, feel free to post again.