Google has been quietly changing the "relevance" of advanced operator searches for some time. The days when they delivered reasonably precise results are long gone. In my experience, inurl has always been subject to a greater number of relevance criteria (i.e. is more likely to "hide" results that Google is aware of) than, for instance, site searches, but all of those types are now unreliable and by default will "hide" numerous results that are no longer considered relevant.

With creative searching, you can often uncover what the hidden content is, so you can assess whether or not it is of concern. Often, the results are robots excluded pages, long removed content, redirected pages and the like which will have no negative effect.

try "drill down" searches like the below and see what you can find:

site:example.com/subdirectory
(you can use prefix-matching with any site: search, as long as you end the string at a point where Google believes there is a word separator)

site:example.com inurl:word
inurl:example.com -inurl:word
inurl:example.com -site:example.com
site:example.com -inurl:example.com (should return no results, but you'd be surprised ;))

Many other combinations are possible, of course.

To directly answer your questions, yes there are problems with the operator - it does not return the results you may expect if precision is what you want. I'm not aware of any major changes to results for this particular operator recently, but bear in mind that determining relevance for this type of query is tricky - some results will always fall off the bottom of the scale.