F9000 contains the task information; task ID, program, version, etc.
F9001 contains the task relationship; the task view, the parent task number, the child task number, and a few attributes, not much else.
F9002 is the Alternate Description for a task. There are a couple of other Alternate Description tables as well (F9005D, F9006D).
F9005 and F9006 contain the Variants; these records either enable or disable a task for a given role. This was at one time called "fine-cut".
What you may be describing are "orphan" task relationships. It can happen as follows: A "tree" of relationships is constructed such as:
E1 menus
--Logistics
----Sales Order
------Daily Processing
--------A New Task Here
If someone deletes the relationship between the second level (say Logistics) and the third level (say Sales Order) then the task containing program information (A New Task Here) has become an "orphan". It still sits in the F9000 table and its relationship to its parent (Daily Processing) still exists in F9001.
And that maybe what you are seeing. I don't know a GOOD way to clean these up.