I've succesfully installed a few flatpak apps from the flathub repo, on Kubuntu 18.04 64bits.
Only problem is that the apps that require browsing through local files use a nautilus-like browser instead of dolphin, which isn't great because my favorited folders don't appear on the side pane, and sometimes links to my ntfs partition (shared partition with Windows where all my personal files are) just don't work. I'm using Kubuntu.
So I've tried uninstalling gnome runtimes
flatpak uninstall org.gnome.Platform//3.26 (along with 3.28) and installing kde runtimes instead with
flatpak install flathub org.kde.Platform//5.9 and
flatpak install flathub org.kde.Sdk//5.9 but that didn't resolve the problem.
Apparently the problem is not linked to the runtimes (truth is I don't even know what a runtime is... :-p ). Zotero was the app needing gnome runtimes as I found out later when Zotero wouldn't launch!
For instance 'Documents' folder is considered as a file, and I can't open it. (This happens on Zotero only. With LibreOffice they appear as folders but I don't have access to favorites)