While it doesn’t answer the “how so fix it” questions still a quite important note:
Please note that this is a commit of the current “master” branch where all development is happening. This branch might show unexpected behavior or could even break at any time.
If you don’t want to contribute to the development of GVM and want to have the best experience with GVM it is strongly suggested to stay with the official announced source code releases in About the Greenbone Community Edition category - Greenbone Community Edition - Greenbone Community Forum.
After switching to a stable release and if the same messages are showing up there you could open an issue report to the development team working on the GVMd at Issues · greenbone/gvmd · GitHub
Keep the following in mind when using SQLite3: Gvm-cli connections fail under openvassd load · Issue #347 · greenbone/gvmd · GitHub. Switching/migrating to the PostgreSQL backend might be an alternative as well.