Unfortunately i don`t know which Zip- Prog you use.
Personally i use Winrar, so i`ve you Unzip a Zip-File you have 3 Unzip Options from which to choose:
Extract files
Extract here
Extract to ...... (folder)
So if you use Extract here while the Zip Archive isn`t a Folder but a bunch of Files (Manga Sites) the Prog will simply extract all Files to the Folder where your Zip-Archive is located. For this cases you need to use Extract to ... (folder) which creates a Folder in which the Files will be unpacked.