That would be the "Open Rebellion" random event. It can occur on planets with low allegiance periodically, though it seems it is somewhat bugged (seems to be happening too often, and TEC Rebels shouldn't be able to make peace with them). The devs have said it will be fixed in a patch, in the meantime you can prevent it by toggling all random events off.
As for mods, you shouldn't have to worry about if they support the DLCs. Any modder worth the name will either have the DLCs worth with the mod or disable them if they interfere (it doesn't really make sense for a Mad Vasari Titan random event to occur in a Star Trek total conversion).
If you want mods that add new stuff, the Enhanced 4X Mod and Distant Stars are the main "Enhancement" mods that add new stuff like planets, research and customization options among many other things, but not new races. At the other end of the spectrum you have total conversion mods like Sins of a Galactic Empire (Star Wars) or Sacrifice of Angels (Star Trek) that replace all the Vanilla races and add new custom ones. This is a nice list of major mods that clearly shows what they do, just make sure they have a Rebellion icon.
