1.0.1.141 Extra Copy of Luxury

If you improve a luxury then settle on it, it increases your copy number of that luxury by 1 over the expected number. Save game provided to demonstrate (Marble; my second city settled on it). It does carry on when reloading. Note also that this isn't the first game where I noticed this - I neglected to post the other save game because I was using several mods.

I had a similar case using a strategic resource. I had a 7 Coal source (my only source), which I used one of to build a factory. Pillaging the tile brought me to -1 Coal. Putting a GP improvement over the pillaged mine brought me to -8 Coal.

Weird.

I'd imagine in my case, the game neglects to read the luxury as improved before crediting me with another. In your case, it seems that the game reads the resource as improved, making the GP improvement take away 7 of that resource, even though the 7 was already deducted due to the pillaging.