Hmm, I just made a sample table and your query seems to work as written:
sqlite> create table statuses (word_id, status default -1);
sqlite> insert into statuses (word_id) values (1);
sqlite> insert into statuses (word_id) values (2);
sqlite> insert into statuses (word_id) values (3);
sqlite> insert into statuses (word_id) values (4);
sqlite> insert into statuses (word_id) values (5);
sqlite> select * from statuses;
1|-1
2|-1
3|-1
4|-1
5|-1
sqlite> UPDATE statuses SET status = 0
...> WHERE word_id = (
...> SELECT word_id FROM statuses WHERE status = -1 ORDER BY RANDOM() LIMIT 1
...> );
sqlite> select * from statuses;
1|-1
2|-1
3|0
4|-1
5|-1
So, in other words, your query is right - your error is probably elsewhere in your code.