I've had similar issues, mostly with recently created communities on other instances and I couldn't quite pin down the conditions causing it. You can include the @instanceurl suffix in the search and sometimes it helps, but the workaround that works best is to access the community you want directly manipulating the URL, so in your example http://lemmy.ml/c/[email protected]
My workflow has been:
search browse.feddit.de to discover the most popular communities I'd like to join
Well yeah, but lets say that I just want to search for whereisthisplace over all instances and see where this community is (even on multiple ones).
The only other approach is to go to each instance and search for it.
But my question still remains - why some communities are shown (eg.: Apple) and some are not (eg.: whereisthisplace)