To reproduce:
1. Open attached project
2. Open CaretBug scene
3. Press play
4. Enter something in input field
5. Notice that input text caret is below input field ( http://prntscr.com/4u5mad )

Input Box Caret is completely off on the Pos Z property of it's RectTransform. This is happening due to the Plane Distance property of the canvas (Render Mode: Screen Space Camera). If Plane Distance is set to anything other than 0, the caret will be completely off on the Pos Z. If set to 0 everything positions correctly.