You can't.
The stuff from STEAM contain additional patches, as well as DLC content that isn't included in the DLCs themselves. Usually, scripts and .ini changes. And there's no way to disable STEAM from automatically downloading it, outside of permanently keeping it in offline mode and never buying any other game that uses STEAM.
What you're experiencing seems to be temporary data: i've noticed that when STEAM updates stuff, it contains a lot of data for the download that is then automatically removed once it's complete. I have no clue why STEAM does this, but several times my computer shouted at me when STEAM was updating that I have less tham 250mb on my HD, even when I have at least 3 gb free.