While the filesystem issue showed stubbornness, the fact that it tried to build a catalog is perfectly reasonable, given it is an ebook management software, which happens to include an epub reader.
You really can't blame a program to do what it says to do.
I don't blame the program, I blame myself for installing a management software when all I wanted was an ebook viewer (and definitely NOT a management software of any kind).
FYI: Calibre contains a program appropriately named "ebook-viewer" that allows you to view a file (like an epub) without all the library management stuff.
You really can't blame a program to do what it says to do.