See bug report at https://en.wikipedia.org/wiki/User_talk:Citation_bot#Bot_has_been_logged_out.
From the talk page:
Or it could be that the bot isn't properly handling cookies: it copies the Set-Cookie headers from the initial call to action=login (without correctly handling deleted cookies), then it manually constructs cookies from the deprecated response values which are likely to be failing to be valid anymore with the increased validation of the session data. Anomie⚔ 01:14, 20 February 2016 (UTC)
The bot should be updated to use proper log-in procedures.
Code lives at https://github.com/ms609/citation-bot.