I just upgraded my MBP (Retina, 13-inch, Mid 2014) to El Capitan today. With only light use of ST3 (build 3103), after an hour or so of working with other tools, I got the dreaded “Your system is running low on application memory”. In the list Sublime Text showed (“paused”).
With the dialog still alive, I fired up Activity Monitor and scanned for big memory users. Holy crap, Sublime Text was using 68gb! (not a misprint) This never happened before, when I had Yosemite. Please advise what I can send in to help debug this.