This has now been resolved, categories are working as expected again. Refresh the page if you still see the issue.
If any of you run into this, there’s a simple way to fix it in WordPress, go to Settings, then Permalinks, and change or enter something under “Category base”. Reload the page to make sure it takes effect, and then go back and change it to what it was before (or empty it if it was empty). Then refresh the page again, and it should work as expected.
The original post describing the issue is after the jump…
I think I broke something while optimizing/organizing/”fixing” things, the Category Archives currently show all the latest posts, instead of only posts that are marked to be in that particular category. The Tags are working fine. The Categories are the ones with /category/ in the url, and you can see them on the blog pages as “Filed Under”.
Here’s a screenshot example of what’s broken (the ones with red):
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