There are underlying reasons this happened and you can track it down by examining everything about each scene’s canvas setup and scaling that are different from the other.
But keep in mind it might not be super-easily to address it in the general case, especially if you start partitioning your UI into chunks.
An alternate workflow is to put chunks of your UI into separate scenes and then load those scenes additively.
For instance you might have the following scenes, all loaded additively:
- content scene (the level, including lighting)
- player (including camera)
- the generic UI (score, etc.) (including EventSystem)
- the weapon UI (ammo, readout)
- the pause UI (turned off until you press ESC)
- the Inventory UI
- etc.
By keeping those all as separate scenes, you can get away from lots of code to load prefab chunks here and there.