Are there any matrices like this?
I think yes... choose $B$ to be all zeros except $1$ at an off diagonal component $(i,j)$ that affords $B$ a square root. Then choose $A$ to be a normal matrix where adding $1$ to the $(i,j)$ component makes it defective without a square root.
Of course this is not an explicit example, but I can't convince myself this situation couldn't happen.