General configuration - Defining the scope of the Program
Program's Scope is defined by the range of data which Scope Context User has access to, therefore Program Lead can be any Jira user and despite their level of permissions in Jira environment, they will be able to view this Program along with the allocation of Tasks within its scope (as long as the Scope Context User is granted a certain level of permissions).
Scope Context User
Scope Context User - a user in whose context the whole Program operates. That means that all data used in the Program will be pulled to it, based on the scope and range of permissions which that specific user has.
Programs can be created together with a new project or use existing data available in Jira:
To narrow the scope of the Program, you can use the extra filter (JQL).
Scope misconfiguration errors warnings
The warning states, that you have added a JQL to Program's scope a which leads to an item that does not exist (such as a filter or a project) or you don't have permission to access:
'Scope misconfiguration! A value with ID '10375' does not exist for the field 'id'. user: (...)
To avoid such warnings, run a JQL using Jira issue search first to see if the results are what you aim for in your Program.