Remove excess caulk with a tool designed for this purpose, or just your finger (in our case, it did a great job). Use a damp cloth to clean off any remaining caulk and to smooth the finish. Let the caulk dry, keeping it free from any water contact for the manufacturer's recommended time.
•They work using a water base or mineral spirit base with little particles that penetrate directly into the grout’s granular structure. This liquid absorbs right into the porous surface of the grout. Once the base evaporates away, the latex and silicon, which are water resistant particles, stay inside of the grout, filling in little holes and preventing moisture from getting inside.
•Where showers and baths are concerned, only penetrating sealers should ever be utilized."
Some of our customers request porcelain or glass tiles for custom printed tile murals in their bathroom and shower, due their moisture resistance. But we consider this 'overkill' and suggest less expensive ceramic, as long as installation is done in a professional manner. For immersion service, we do recommend porcelain and glass.
An ounce of prevention is worth a pound of cure. We had the same problem here and I fixed it the same way. Grout in corners just doesn't work. With the expansion and contraction of the house even just from temperatures, the grout doesn't flex enough in the joints. When I do new bathroom renovations, caulk will always be used in the joints.