I actually did the same thing as you... but I also know that stains really are meant to be wiped off. I probably should have looked at dyeing first, but I just let it dry. I sanded it lightly with 220, did it again with no wipe, then used 0000 or 5 O and applied once more. It was super hot and so mine dried over night. I only used a brush. No wipe. This way I was able to get a nice coat on top with no imperfections.
I chose to do this because I like to see the wood grain. Paint will typically hide the grain, so I went this route. BTW, I used MInwax Ebony as well. For my final, I used a Varathane poly to seal it and make it shine. I also used 5 0 or 6 ) to smooth out before I applied the poly. Even though it gets a bit clouldy after "sanding" with the steel wool, the poly will take care of that. Looks awesome.
In my opinion, just sand them out, and apply another coat. Hopefully the bubbles do not continue to come back. If they do, then I would probably take it all off and try again.