What setting material was used? Mastic instead of thinset stains porous tiles like concrete tiles. A sealer doesn't magically repel dirt either. It just makes them easier to clean. But they are very porous, and absorb all kinds of things.

If it has happened over time - it’s just the nature of concrete/encaustic tile. Use/traffic patterns stain, even when sealed. It usually requires a professional stone restoration company to get the stains out. Then reseal. Then do the whole thing again in a few years. Rinse. Repeat. Or, embrace the patina.

thank you so much for responding to this. Thinset was used. I know the sealer wont repel the dirt but honestly other than dust and us with socks on our feet, there's not really any dirt. Tiles that don't ever get foot traffic are the tiles that are becoming the most yellow? I have to believe it's an issue with the sealant. This all happened within a few months. We literally just had the tile installed last June. A few short months later it started to yellow. Also, spots that receive the sun and heat from registers are also more yellow. It's just so frustrating and the money we put into this is insane! I appreciate the advice, I think we will have to have it sanded down somehow and resealed.