Steps to reproduce:
1. Open my attached project inside "case_806527 Raycastproblem" file.
2. Select "Test Broken - Camera too high" scene.
3. Press play button in toolbar.
--- There are two raycasts. One comes from "FPCamera" object and another from "Capsule" object which is always directed into "FPCamera" object.
4. Open console.
--- "Capsule" object Raycast should hit "FPSController" object (because "FPCamera" object is inside of "FPSController" object) and show it on console window but it doesn't.
5. Press play button again.
6. Select "Test Works - Camera lower" scene.
7. Press play button in toolbar.
--- "FPCamera" camera object in this scene is 0.05 lower in Y axis than in previous scene.
8. Open console.
--- "Capsule" object Raycast hits "FPController" object and now console shows this detection.

Reproduced in: 5.4.0b23, 5.3.5p3, 5.3.1f1