Hi Sanjay,
I would have to say that bookmarks and style mapping have caused the most problems for our users.The majority of our contract clauses are not static. It is quite common for users to edit clause text. We found that editing clauses in an assembled document requires a knowledge of MS Word (bookmarking) that most users do not have. Users would accidently remove/add bookmarks while editing and then spend a considerable amount of time trying to fix them so the document could be assembled. Often this would result in the user having to start all over with a new document.
We also found that style maps were not applied consistently and users would have to spend time manually correcting the formatting (which we trying to reduce by using the clause library functionality) in the first place.
Rogue bookmarks also began to appear in the assembled document whenever we edited the contract template and saved as a new version. These bookmarks were added by the system and would negatively impact the document style mapping/outline view display. Admin users would spend a large amount of time removing the rogue bookmarks after each template edit.