I have been having a problem with my pages not categorizing on the wiki we use at my office. Since it is corporate & private, unfortunately I can't share the actual wiki.
When I create a new page, in order for it to categorize I have to save it with no content except the categories. The blocker seems to be any other links in the content of the page. If I created a page with content, categories, and all, it would not categorize. In this case, I have to go back in and cut all the content, saving the empty page with just categories, then pasting the content back in once I see it has categorized. (I also tried removing all link brackets, and that worked, but it's easiest just to remove everything.)
Additionally, sometimes one category will even block the other. I will have to save it first as one category, then add the next one and save again, then add the content and save when it's finally in all the correct categories.
This isn't the worst (although it is pretty annoying) when creating new pages from scratch. But once pages are created, if I want to change or add categories it becomes a major headache.
The other symptom of this problem is that pages won't show up as "uncategorized" if they are in one category but not some of the others, so I can't easily identify which pages aren't categorizing properly (we have a lot of pages).
Here is our version info:
PHP 5.6.24 (cgi-fcgi)