Maybe the mother plant is too young and separating the two shocked both of them. I was always told to leave the first pup and remove the ones that come after. What type of banana are you growing?

I tend to agree, u likely damaged both plants some, and they will most likely come out of it...
Are they potted or in ground?
What mg fert are u usin? Naners like a 3:1:2 ratio, or thereabouts...

Good luck, I doubt u hurt it bad, they r tough as nails!