Course A has a course rule with multiple courses.

The course rule is set up so that the “Use when enrolling Students" checkbox is checked. 
When scheduling students the program assumes that the students also need requests and enrollment in all of the courses that that Course A has a rule with.  If students have a request for Course A but do not have requests for all these other courses it cannot schedule Course A. It cannot fulfill the course rule so it won’t schedule the student in Course A.
The Scheduling rule will need to be changed as follows:
1.       In Configuration>Registrar’s Setup select Scheduling Rules
2.       Open the Scheduling Rule
3.       Uncheck the “Use rule when enrolling students” checkbox.
4.       Save and close the rule
5.       Rerun Generate Student Schedules