For such things I use the discussion plugin. My colleagues use this feature frequently I think because it's just so easy (and intuitive) for them to leave a quick comment on any page without having to edit it and have someone else take care of the problem (which is me). On the start page I use the integration with pagelist to show a summary of recent comments (as links) like so: {{threads>*&table}}
. I restyled and augmented the table to show recent comments on top with name of user who commented last and highlighted in red, if the comment is younger than 10 days (using JS/jQuery, CSS). This way, I can see any newly posted comment when I enter the wiki, and they can better keep track of my answers. This works really well for me and my team. (I should show you a picture. If I only knew how.)
What also comes to mind is the batchedit plugin. It provides a nice summary in the admin panel when you use the preview function to list all entries let's say of some comment section directly from all the pages in the wiki on the click of one button, then you can conveniently edit each item from this central place. To uniquely mark the fixmes, you could use hidden tags on the relevant pages which are not shown on the page but they can be fulltext searched for (by the batchedit plugin), like so: <wrap hide>special tag</wrap>
using the wrap plugin. You could even make an extra toolbar button in the editor to make it easier to drop these notes on any page.
BTW, did you come across the bez plugin. It's a rather complex ticketing system (problem reporting system) which might be possible to adapt to your usecase.