I think I found an issue with the experimental .expert command in the sqlite3 CLI. This is related to generated columns.

The issue triggers when you directly reference a generated column in a query and when a database view mentions a generated column, even if it is not part of any join or where clause.

Consider this schema:

CREATE TABLE SomeObject (
 id_ INTEGER PRIMARY KEY,
 x TEXT GENERATED ALWAYS AS(HEX(id_)) VIRTUAL
);
 
CREATE VIEW ObjectView AS 
  SELECT id_, A.x AS AX, B.x AS BX
  FROM SomeObject AS A
  JOIN SomeObject AS B USING (id_)
;

Running this query works and yields no results (expected). When you turn on .expert, this happens:

sqlite> SELECT * from ObjectView;
sqlite> .expert
sqlite> SELECT * from ObjectView;
Error: no such column: A.x

Note that the generated column is not used in the JOIN clause defined in the view.

Accessing x directly:

sqlite> .expert
sqlite> SELECT x FROM SomeObject;
Error: no such column: x
sqlite> SELECT x FROM SomeObject;
sqlite> 

Accessing only id_ works:

sqlite> .expert
sqlite> SELECT id_ FROM SomeObject;
(no new indexes)

SCAN TABLE SomeObject

sqlite> SELECT id_ FROM SomeObject;
sqlite>

Used versions:

SQLite 3.35.0 2020-12-07 23:14:25 4b286129138d44e6f8e9b3450289941e01d20fdfb9d0b5d846031425e8ca6b49
zlib version 1.2.11

This also happens in 3.33.0, as shipped on Ubuntu 20.10.