Over my years at Microsoft I have encountered what I'd like to call the work item copy anti pattern.
What happens is that the team members tend to copy work items rather than creating new ones because there are several fields that have been configured as mandatory but some authority. Since it is a pain to fill these in each time the team just copies and old item with all fields set correctly.
The result is that the new work item typically have some fields set wrong because the user forgets to change it. But even worse the source work item typically ends up with a link to the new copy. A link that is useless since the copy most of the time has nothing to do with the source item. So now you have a bunch of work items that have links that are irrelevant and in worst case actually hides a real important work item link.
I think the reason why this happens is that TFS workflows are setup for larger organizations than just individual teams at Microsoft. And I have worked in small organizations at Microsoft and the workflow is still not suitable for all teams in that organizations since teams like to (or need to) work slightly differently. Another important factor to why this situation emerges is in my experience that the team is adding too many things to TFS creating a need to quickly create a lot of work items to track their work.
Let's assume you are stuck with the tool and the process I have found a very simple solution to the problem. And remember this is assuming you just have to do it. Obviously the first priority should be not to do it. But remember... You're stuck with it... The simple solution is Excel. You can easily open a TFS query in excel and add and remove columns there as needed. Just use excel to bulk add all your work items and focus on the stuff the team needs. Then one person can cut-n-paste all the mandatory fields needed. Still you end up with some errors due to the cut-n-pasting (we need to leave a motivation to fix the process, not just the symptom...) but at least those pesky false links are not in there for sure...