From looking at the save, there are many enemy bases, split between EXALT and Black Lotus (and one actual alien base). I'm not sure which is the one you mean, but have you tried patrolling the area with a vehicle?
Yeah, I've tried both France and South America, but found an alien base in India after I decided to proceed game from the save, where is no such message (save2), because I afraid of further bugs, which could be caused by this one.
Just in case, you've noticed, that the message tells about France in South America, but it is actually in Europe, right? This is the essence of the bug.
And did I understand right, that these messages could mean not only alien base, but anyone else base?