Each icon you see in the Applications overview corresponds with a .desktop file that provides the shell with various information on the application, including the name to display in the menuing system, how the program should be launched, and obviously also what icon should be used to represent the program. These files are merely text files. The information on what icon to use is provided on the Icon=
line. There, you can specify either the full pathname (i.e., folder and subfolders + name) of any compatible graphic that you want to be used as an icon or only a file name. In the latter case, a valid icon file is looked for in some standard folders. If no icon is specified, or no valid icon is found, a fallback icon is used.
Thus, you should check the corresponding .desktop file, and ensure that 1) there is a line for the Icon and 2) it points to an existing valid file.