No, I do not think it a hardware problem.
First off, my main encounter of this problem has been on a Mac Pro (i.e. not a MacBook Pro).
Secondly, since 10.11.2 came out, it is happening much less frequently on my Mac Pro (around four times total since 10.11.2 as opposed to daily before). Also, my MacBook Pro (2015) is not having the problem at all (which might imply a hardware (or better put, firmware (e.g. BIOS)) problem for others).
From watching this case, I can only assume that there are no Apple 3rd party debs in this litany, else, someone would have opened a bug report against 10.11 telling Apple that it is "affecting their product's development" or some such wording. I am a member of the Mac dev program but am not any help as I said it's occurring far less frequently (e.g. Apple will always ask a dev if they have the most recent OS/code installed and if not, put it on before they will address the case).
If it becomes repeatable enough though, I will open a case and see if I can get some attention to this egregiously quality-poor problem.