There are few things that can cause this.
Duplicate Categories trying to use the same URL, upon reindex Magento will auto increment these values. To the next higher integer.
It's sometimes easy to miss.
Say you have the category "shoes" as a subcategory of "women"
The URL key created automatically for this category would be "/shoes"
Now say you have the category "shoes" as a subcategory of "men"
This category would automatically have the url key of "shoes" however because it already exists Magento will auto increment this key to "shoes-1"
Under a multi-store instance of Magento, you also can't have two categories with the same url keys even if they are part of different stores.
Additionally, Magento Enterprise 1.13 has a whole different problem with auto increments of URL Ids
What version of Magento are you running and is it a multi-store platform? I can provide further assistance from there.