If you are trying to Assign Items to files that share the same Part Number you may have noticed a peculiar behaviour. Consider the following Assembly...
When you assign Items in Vault Professional 2012, using the "Auto-select first duplicates" option you can see this result.
Notice that the last Item Number for the 444.ipt file, will be replaced another Item Number, 100001. But 100001 will be replaced with Item Number 123456, causing a cyclic relationship. Indeed, if you click Finish at this point you will get this message.
The reason this happens is the Item Assign wizard will query the database for any existing Item Numbers that have been already committed. Because the Item Number 123456 has not been committed to the database it won't be returned by the query, causing the behaviour.
Autodesk is considering improving this behaviour in a future release.
The workflow to overcome this would be to either:-
A) Before assigning an Item to the assembly, Assign Item to one of the children first, or..
B) Right click the "Replace With" cell, Click "Select Replacement Item", then untick the Item Number 10001, or whatever it is in your system. This excludes it from being included by the "Auto-select first duplicates" subroutine.