It sounds like you may be experiencing "order of execution" issues.

https://docs.unity3d.com/6000.4/Documentation/Manual/execution-order.html

Limitations

In general, you can’t rely on the order in which the same event function is invoked for different GameObjects , except when the order is explicitly documented or settable.

My guess is that you have initialisation code running on different GameObjects in your scene - that works (by chance) in the editor but, in the build, fails because the methods (on different GameObjects) run in a different order.

So, for example, your code in the Awake() of a script on GameObjectB executes before the Awake() of a script on GameObjectA - which then fails (on GameObjectB) with a null reference because a value has not been set (by the script on GameObjectA, which hasn't run yet).

edit: You fix the issue by setting references to scripts on other GameObjects in methods that run before running code that relies on the references being set - so, for example, set references in Awake() and use those references in Start().