Yellow stains can be caused by a chemical reaction between non-skid backings, non-skid mats, rubber, latex and other plastics. These stains are largely permanent.
To prevent these stains from appearing or worsening, switch to a vinyl-backed mat or color safe cloth mat. Floor is well-sealed and the stain has not permeated too deeply, it may be possible to apply a citrus-based cleaner that is lightly abrasive. You can use either a commercially available cleanser or apply a solution of 2 TB of lemon juice and 1 TB of baking soda applied with a clean sponge dampened with water.
After rubbing area carefully to alleviate the stain, rinse thoroughly with water and pat dry. Once dry, carefully apply a commercially available vinyl floor sealant to the problem area according to the manufacturer's directions.
Caution: Do not use ammonia on vinyl floors as it is corrosive to vinyl. Never mix cleaning agents or chemicals, the result can be dangerous or deadly. Before cleaning, always test the agent on an inconspicuous location to determine its suitability and to make certain it does not damage the material. Wear appropriate clothing such as gloves and protective eyewear, and work in a well-ventilated area. Accidental inhalation or ingestion of cleaning agents can be hazardous and even fatal, particularly to pets and children.