Here is the list of problems I faced in using confluence for writing documents and then converting them to word or PDF.
1. Master/Slave versioning:
if you have a master document which consists of several child pages, each of them will have their own version history. consequently you cannot use versioning that comes with confluence for parent/child pages, unless you are happy with having several change history tables, with different version numbers in the final document.
2. Offline usage
You cannot work on your documents where you are on a train.
3. Loosing content
Ok, this is only one time experience. After half an hour working on documentation, I got a horrible error message “you have enough credentials” and all my work vanished.
4. source control
you cannot push your documents in source control. This means that you have to keep the source and the documentation in sync manually.
5. fine grained versioning
I don’t really want to increase the version each time I change a comma in the text. As far as I know there is no tool, to let me decide when version should be incremented.
6. hard editing
If I find a typo in my docs, which I often do, and I want to correct it, I need to scroll up to the top of the page, press edit button (this can be done faster by keyboard shortcut), scroll back and find the typo and correct it, then I need to scroll down to the bottom of the page and press save (For the last part I think ctrl-s is a keyboard shortcut). This can be cumbersome in long documents.