All DLC will allow you to enter the giveaway regardless of whether or not you own them (as long as you own the base game), you either need to block them from showing if you know you own them so you don't accidentally enter them. Or you need to check each time you enter. This has to do with the way steam interacts with 3rd party websites, it's not SG's fault. One thing that helps a little is that SG keeps track of what you entered and won, and at least the DLCs you've won before will show you that you have won them and cannot enter the giveaway for (you'll still see them in the list of available giveaways unless you turn that off though).
This issue can also impact enhanced/deluxe/other-stupidly-named editions of games as well if that edition of the game is basically a bundle of base game+DLC.