I'm a newbie to refinishing. The guy in the stain/paint department said I could use a roller to apply stain. Now there are bubbles in the finish. Any ideas?

The guy said roller for STAIN and youy're saying bubbles in the clear finish? Do you see the problem here? You're comparing stain and clear floor finish as one and the same and they are not. SOME floor finishes can be rolled on with the correct roller. Not much choice but to sand out the bubbles and redo. This time try a Padco Paint applicator in a 10" size. Easier in small to medium areas. Or use a 3/8" nap white dove roller.

I realize I mis-stated the problem. I rolled the stain. I haven't gotten to the finish yet due to the bubbles in the staining process.

See if you can reactivate the stain by applying more stain with a rag and rubbing hard. Try it first in a small out of the way spot. If that doesn't work, then rescreen the floors and restain. Use rages this time and only apply to small three foot sections that you can remove the excess within about five to ten minutes. Good luck.

I think the staining process directions are very easy to misunderstand. The directions on the minwax stain says to "wipe off excess". I wiped off the excess when I applied the stain, but it appears one has to wipe it close to dry after five minutes. Otherwise you see these bubbles or the stain doesn't dry quickly. I simply used paint thinner to get rid of the excess and thankfully there was no color difference that I could see. But, it is likely that one might see color differences, so this may be difficult to do.