Pure silicone is generally not very flexible. A sanded siliconized latex caulk will give the appearance of grout, but have some flexibility to expand and contract with the changes in temperature. They should have used it the first time, but at least they are coming back, right? If you liked the looks of the original job and the cracks which bothered you disappear, that is all you can ask. Ask them to leave the rest of the tube with you when they finish. You will need to address the caulk about once annually. It is just one of the joys of home ownership. Good luck!

They used siliconized acrylic sanded caulk (Color Fast Industries) that they color-matched with Ardex grout. They left the tube with leftover caulk with me.

So, should I ask them to remove the caulk and grout from the corner before re-applying? I just want to find out what is the proper way to fix it. Thanks.

After installing hundreds of showers, we determined that pure silicone, to match the grout, is the best. Siliconized latex and sanded caulk will fail quickly, and fail often. The installers do have to completely rake out the existing caulk and any grout, in the inside corners. Then re caulk. Be sure the shower is completely dry before and after the job is done.
Tile contractor

In addition to it being totally clean and dry before they start, you won't be able to use it for at least 24 hours after they come to make the repair.