The two tables are probably on two different connections which requires two separate refreshes. I think if the two tables are related, it is best to join them under one data connection to avoid such scenario.
However, if the two tables are already on the same connection, then it is very strange for the two to not being refreshed together.
Hope this helps.
There is an option to refresh all extracts used by a workbook with a single menu action in the Tableau 6.1 beta, so I think it's a pretty safe bet that that option will be there in the official release of 6.1, which I think is expected fairly soon (probably a matter of weeks, I would guess).
Thank the deity of your choice! this was driving me nuts very quickly, especially with duplicated connections...