Caulking corner of showers changed grout color
Generally speaking, any time you apply a glossy material over a matte material you get darkening. It's unfortunate that this was discovered now, but you do have options. 

If you haven't yet sealed the grout, and plan to, see what that does for the situation. Some sealers won't change the color, but some will. Maybe it'll bring things closer to a match.

Otherwise you'll need to cut away the caulk, scrape off at least the surface of the grout (deeper is better for bonding), and re-grout those joints. 

Clear silicone is great for many things, but color-matched caulk is better in this situation, and urethane is the best I've used in terms of grab and durability. Use as small a bead as possible (trim the nozzle to act as a tool and don't "finger" the bead out), and note that urethane does not come off what you put it on. Plan well, wear latex-type gloves and old clothes, and consider masking the tile outside the bead boundaries.