Generally one doesn't stain over top of finish. That's a process that we call "glazing" or "tinting" which is stain mixed in with clear finish.
Your table came from the factory with a catalyzed urethane (nearly all production furniture is finished this way). Depending on what finish you used, and it's compatibility with the original finish you may have a reaction or loss of adhesion going on. To remedy you'll need to start over by sanding to bare wood, then stain, then finish.
I like to use sanders that hook up to a HEPA vacuum, and then stick with one brand of stain and finish. I've been using General Finishes gel products lately. Look good, very durable and easy to work with. IMHO & experience Varathane is crap.
Charles Freeborn | Fine Furniture