Example as below. I noticed this with a better-sqlite3 upgrade to 11.9.0 which included an upgrade to sqlite 3.49.1. I have also confirmed that it's still present in sqlite 3.50.2. Shifting the comment into the window definition instead works.

-- Create and populate a test table
CREATE TABLE test (x INTEGER);
INSERT INTO test (x) VALUES (1), (2), (3);

-- This works:
SELECT x, ROW_NUMBER() OVER (ORDER BY x) AS rn
FROM test;

SELECT x, ROW_NUMBER() OVER (w) AS rn
FROM test
WINDOW
  w AS ( -- this comment is fine
    ORDER BY x
  );

-- This fails with: "near "WINDOW": syntax error"
-- because of the comment between WINDOW and the window definition
SELECT x, ROW_NUMBER() OVER (w) AS rn
FROM test
WINDOW -- this comment breaks it
  w AS (ORDER BY x);

Output from the above looks like this; unsure whether the layout change (the newlines are not as per the source file) are significant.

sqlite3 < tmp.sql
1|1
2|2
3|3
1|1
2|2
3|3
Parse error near line 18: near "w": syntax error
  S rn FROM test WINDOW -- this comment breaks it   w AS (ORDER BY x);
                                      error here ---^