See https://commons.wikimedia.org/w/index.php?title=File:Teatrul_%22Ioan_Slavici%22_Arad_-_vedere_frontala.jpg&oldid=77018984 This images has a perfectly acceptable category, Historical monuments in Arad County, coming from {{tl|Monument istoric}}, but was also marked as uncategorized.
This should not be the case
Version: unspecified
Severity: normal
Hm. We'd presumably need to call the parser over the API to make sure, and that seems like a lot of overhead. But I'll look into it.
As I know, this function is intentional and useful. Topical categories should be never added through templates but should by manageable by Hot-Cat and Cat-a-Lot, category-renaming bots etc. if needed to move the files to more special or more suitable category etc. Categorizing through templates should be used only as tagging for technical flat categories. The linked example was really not properly categorized. It is not categorized by place (Arad) nor by the subject (theatre) nor in the category tree of Romanian heritage monument but only in some flat categories. It's quite OK that bots or UploadWizard marks such files as uncategorized.
SJu, what you said might be true for Commons at this point in time, but UW should not be written specifically for Commons. For instance, since this summer UW is active on ro.wp and on that wiki topical categories can be included from templates.
I have to agree with @SJu, as much as it pains me to say it, Commons is kind of the main client for UW, and this is the right behaviour for Commons. Maybe later we can write in a config option, but right now, this is low priority.