Yes, it means the upper atmosphere is cooler AND they cannot explain it.
I find these plots interesting:
Frames (a) and (c) are of the upper atmosphere density; frame (b) is the sun's radio intensity at a wavelength of 10.7 cm, a key indicator of solar activity. Over the years, the minimums in frame (b) remain quite constant, but the minimums in frames (a) and (c) get progressively lower, with the latest minimum lower than even what the trend (the green line in frame (c)) would predict. Something else beside the solar miniums is making the upper atmosphere cooler, it seems.