The shell(s) in the pix look fine and show healthy new growth. If the tortoises are acting all right, I would not worry about this coloration issue at all.
Gentamicin is very hard on reptile kidneys. I would not use on any of my tortoises it even if there were an infection as there are better choices available today. Make sure you keep them extremely well-hydrated for the next 2-3 weeks so the medication doesn't crystallize in the kidneys.