I noticed that when I open the Expenses by category over time report form, uncategorized transactions have a tick on by default. At the same time all other categories are off by default. Uncategorized transactions are in the end of the list so when I see the list it seems like no categories are marked (which is totally sensible). Hence I mark a few categories I am interested in and build the diagram.
The unpleasant thing is that this diagram is misleading, because uncategorized transactions are included. I figured this out purely by accident.
I think this is incorrect behavior. I suggest that in all reports demanding categories to be chosen all categories should be disabled by default.
P.S. I noticed that the "Categories" field in the form by default says "Not chosen" (I am not sure about English translation, because I am using the Russian localization). Hence the fact that uncategorized expenses are on by default is definitely a bug.
Thank you, Pawel.