They sure look like two entirely different plants to my eyes also but my eyes aren't what they used to be.
You could dig the entire thing up and gently remove all soil from the roots and "tease" the roots apart to see if perhaps you do indeed have two separate plants. If that were the case I'd pot each up separately and watch as they mature to see what they turn out to be. My first thought was possibly a Cassia seedling for the small plant but it's not that.
There are a few varieties of Acacia that grow in the San Diego area. I googled for seedling images and found a couple of photos for comparison:
https://plantasmagorical.files...
http://upload.wikimedia.org/wi...
Scroll down this page for listings and photos for San Diego Acacia:
http://www.calflora.org/cgi-bi...