The reason for this is most likely how you've mapped the categories for iSnare and your own together. If you go to Settings > Receive Articles and look down the bottom under 'Mapped Categories' it will show you how you've got the categories configured. If the list is long and repeats every iSnare category on the left with every one of your category, then this is your problem.
You can fixed this by clicking the "Remove All" link. Then click 1 iSnare category then click 1 of your categories you want the articles to go to for that category, then click 'Map Categories'. You'll need to do this for each category.
If you select all the categories in both boxes, it will do as what you have now, mapping every iSnare category with every one of your categories.
For the articles that have already been submitted, you'll need to edit them to change what category they are in.

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