Someone found a fix for this, by the way:
The workaround is as follows. After you defeat the alien base, when you attempt to make the hyperwave beacon the game will tell you that you need x2 hyperbeacons to make the facility which is impossible to get since there is only one in the game. You will have to edit the .mod file and look for "SW_MARATHON=2.0f" . Set it to "SW_MARATHON=1.0f" , load the game, make the facility, save and close the game then edit the file back to 2.0f.
(Source:
http://xcom.nexusmods.com/mods/7)