Wait, so they wanted to replace the SSD? Or the Mac itself? They said it was software related but couldn't tell you any more? And the original OS was Lion?! You must have the Mid-2012 15" rMBP. That's a 4 year old machine.
Hardware can suddenly fail. Again, correlation does not equal causation. Plenty of people's 2011 15/17" MBPs began to show signs of the GPU failing straight after upgrading to El Cap. This does not mean that 10.11 caused the graphics issue. It just made it apparent.
Furthermore, SSD technology in 2012 was comparatively in its infancy. The failure rate was much higher. They could support less lifetime writes. Plus your model has
documented issues with the GPU failing.
Unless you can elaborate further on what exactly was said/done to make you think it was a software problem – or even provide the Genius Bar report, and why they couldn't just reinstall the OS, which is what would resolve a
software issue – I'm afraid I'll have to take what you're saying with a pinch of salt.
EDIT: I appreciate you said that the problem reoccured after updating to the latest OS. But again, that doesn't mean the OS is to blame. 10.11 is much more graphics-heavy than 10.7, with all its animations and features. Also on your model, it uses Metal rather than OpenGL. It could just as well be the graphics card creating the issue. In fact, as I write this out, I'm more convinced that's probably what's causing it.
EDIT 2: Lemme grab an expert opinion!
@Weaselboy, what do you think, if you'd be able to have a quick look over what they described? Graphics card or something else?