In case the paste bin expires, here's the result:

mysql> select distinct tl_from from templatelinks left join page on page_id=tl_from where page_title is null;
+---------+
| tl_from |
+---------+
|    3364 |
|    3612 |
|    3697 |
|    3722 |
|    4996 |
|    5055 |
|    5136 |
|    5139 |
|    5497 |
|    5506 |
|    5508 |
|    5729 |
|    6088 |
|    6093 |
|    6098 |
|    6099 |
|    6100 |
|    6102 |
|    6104 |
|    6106 |
|    6109 |
|    6110 |
|   14604 |
|   14628 |
|   14629 |
|   14822 |
|   16128 |
|   16228 |
+---------+
28 rows in set (7.59 sec)

Simplifying people's work, could you please run the following in pt.wiktionary:

delete from templatelinks where tl_from in (select distinct tl_from from templatelinks left join page on
page_id=tl_from where page_title is null);

Thanks.

(In reply to comment #2)

Simplifying people's work, could you please run the following in pt.wiktionary:

delete from templatelinks where tl_from in (select distinct tl_from from
templatelinks left join page on
page_id=tl_from where page_title is null);

Thanks.

Done, was only 60 rows anyway.

60 *nasty* rows that were messing with our Special pages :).
Thanks, Roan! Let's see if the Special pages reflect this change in the next day or two.

Fix confirmed. Closing bug.

(In reply to comment #3)

Done, was only 60 rows anyway.

What about other wikis of WMF? It is possible to check each project? Thanks.