The time stone is one of the 6 infinity stones and it along with the soul stone is one of the last two remaining stones that are yet to be discovered and much like the space and mind stones, the color of the time and soul stones may alter from their comic book colored versions and these are the reasons to why the time stone may slip up here in the upcoming Captain America Civil War;
1. After Joss Whedon made Ultron kill off Quicksilver in Avengers Age of Ultron out of selfishness, we cannot risk having the Russo Brothers kill off anymore heroes until the upcoming Avengers Infinity War Part 1 and 2 films because I am sure that we are all gonna want to see more of them in more MCU films after Civil War and because there is more that we wish to learn about each of them, especially those like Scarlet Witch who still has more off her MCU history to share with us and since it is a fair and agreeable mystery to why she and her brother Quicksilver survived Baron Strucker's experiments and since the prequel comic to Age of Ultron mentions the twins to be descendants of Inhumans and now because she's the only member of the Avengers to have obtained her powers from the mind stone she is sure to make it through Captain America alive and will be expected to appear in films like Spider-Man where she would share some things that she has in common with the wall crawler as well as for us wanting to see Captain America and the Avengers that he is with in Phase 3 last up to the upcoming infinity war films
2.Because Marvel Studios had focused such heavily dramatic attention on the 4 infinity stones revealed in the first wave of Marvel films and with Kevin Feige making some daring changes in the films that separates their plot from the comics, it wouldn't hurt to actually have this kind infinity stone to show up in this film
3. By having the time stone featured in this film, it would be sealed in an antique hour glass and its power would activate during Captain America's struggling fight with Iron Man, sending Rogers back in time to a day or two before confronting Crossbones in Africa, he would experienced deja vu but would also take the oppertunity to have the team improve on their battle against the villain and his goons by making sure that there are no or less civilian casualties, therefore preventing the government from attempting to regulate control over them which leads them into battling their friends and allies and wiping eachother out
4. By having the Time Stone appear in Captain America Civil War, not only will it help keep other films from having all the fun spoiled until Avengers Infinity War part 1 and 2 but it will also help make sure nothing else goes disappointing by having all the previous reasons for its appearance in this film to be successfully accomplished and that all the heroes in this movie should be available for the Infinity War films
Now while the time stone is yet to be confirmed for the upcoming Captain America Civil War film, we need to make sure that the Russo Brothers do not kill anyone of the heroes off in the film so stay tuned until more updates surface