Volospin,
These 'hand-made' graphics available by independent authors off the web generally come in two formats - straight out graphics files that are collections for scenario / modpack use (such as allflags.gif) or scenario files themselves, each serve a different intent.
Graphic Collections such as those found at sites such as
csc.apolyton.net/icons.shtml are designed so you can select an icon image within the larger graphic collection to be copied and pasted over the existing Civ2 file. They are not designed to substitute for the Civ2 files per se, but just to be used for isolating individual icons to be pasted over the top.
You have found some graphics with blank spaces. These are probably scenario files where the scenario in question does not use the specific wonder of the world, city improvement, city style, flag, unit, etc. In order to avoid confusion, some scenario authors remove superfluous images from within their scenario's graphic files.
Please find the following link to the Scenario League's Design Tips section that looks at a few guidelines on 'art and graphics';
sleague.apolyton.net/Guides/sldt_sort_group.shtml
Remember, when manipulating such files, don't overwrite the original Civ2 graphics - copy and paste icons.gif, cities.gif, people.gif, units.gif, or whatever into a different folder.
Which graphics program do you use?