With new macOS Mojave Apple have developed new security protection for apps and data. Now apps cannot access data from another apps even if it successfully accepted as exception from Apple. BookmarkApp for Safari access bookmarks of Safari and that's why it should be granted for access of such data. You can easily grant access for bookmarks of Safari if you add BookmarkApp in Settings of Mojave. Launch System Preferences, and select the Security & Privacy preference pane. After it select Privacy -> Full Disk Access an then add BookmarkApp in list of apps. Now you can use BookmarkApp on macOS Mojave.