Did you purchase the saltillo sealed or unsealed? If unsealed, more than likely the moisture from your setting material was absorbed into the saltillo from the bottom and you're seeing the water marks from that in your saltillo. If this is the case, you are s.o.l. and will need to replace the tiles.
If you purchased sealed, you will need to contact the company where you bought the saltillo and press them for replacement due to a defective product.

If you want to get creative, I have seen where people have stained the saltillo a darker color and resealed atop...but your water marks could still show up.

Cracks can be filled with a grout that is similar in color. If hairline cracks, use non sanded grout. If large cracks, use sanded grout.

Don't tear them up - there could be hope for those floors! If you haven't done anything yet, do you know any history for the floor? What has it been waxed or sealed with previously?

If you can get to a point where you're able to seal it with a 10-15 year sealer - similar to what we offer our customers (and we're experts in Saltillo tile) - then your maintenance issues go away... at least for awhile.