Was the stain poured on them to where they got wet?

Moisture problem. It could be humidity or something leaking. Is it in the kitchen?

Photos would help. Moisture, moisture, moisture. What is your subfloor? Concrete, plywood, OSB, what is the material? Where abouts do you live? How was it installed? Glue down, nail/cleat/staple, floating? What are the DOCUMENTED moisture readings (written out and handed to you by your installer) for the subfloor? And the documented moisture readings of the hardwood (again, written out all nice and pretty and handed to you)?

No documentation? Ask your installer for your copy (you pay for the work, you get the paper work that supports the warranty). Installer doesn't have them...or looks at you funny and says 'Huh?'...get a new professional involved and do it again.

Start with documentation from the installer and then let us know the answers to the questions when you have a minute.

@marthabonin
Please explain 'cupped'. Has the flooring done this before? What kind of stain did u use! Oil based,waterbased? Did the guy u hired document the M/C of the flooring? Was there a major nature event? Rain,hurricane,flooding? What IS the subfloor ?