As I understand, these icons are stored in two sizes: a small one that's displayed on the profile page, and in the activity feed, and a large one that's displayed on the game's details page in the client, and in the "achievement unlocked" notification. The TF2 achievements from the two cities and the love&war update have extra large images for the large version (about 256x256 instead of 64x64), and they are not scaled back to the expected size, therefore, only the center of the image is displayed. Sometimes these are not displayed at all, just a black square is shown instead.
As I understand, these icons are stored in two sizes: a small one that's displayed on the profile page, and in the activity feed, and a large one that's displayed on the game's details page in the client, and in the "achievement unlocked" notification. The TF2 achievements from the two cities and the love&war update have extra large images for the large version (about 256x256 instead of 64x64), and they are not scaled back to the expected size, therefore, only the center of the image is displayed. Sometimes these are not displayed at all, just a black square is shown instead.