15" Mid 2015 MacBook Pro crashing, freezing and restarting whenever I use downloaded software

I just bought a new Macbook Pro a few months ago, and ever since I upgraded to El Capitan, I've been experiencing issues. See, the whole reason I bought it right before El Capitan's release was to make sure I could upgrade my OS, because my last computer was stuck on Snow Leopard since every time I tried to update to Mavericks or Yosemite, it literally destroyed my computer. Apple wouldn't acknowledge the problem since I was out of warranty, so I wanted to make sure I could upgrade this one while still under warranty.

Anyway. So, my latest issue (already had to deal with a constant battery drain in sleep mode but that's mostly fixed now) is that my computer will periodically freeze, crash, or restart itself. It happens a couple times a week, and I've noticed it's usually happening either when I'm using a downloaded software, or I have a downloaded software open. Example being Photoshop. I'd try to update some pdfs, and I couldn't get more than two lines in before my computer would freeze. Literally took me about an hour to sign a document with my tablet. Another example being Minecraft. This one usually lasts a while but it did crash a few times while playing. The problem doesn't happen often enough that I can recreate it on command, so I can almost guarantee the Genius Bar will be as useless as they were with my last laptop and tell me to factory restore it (literally the only advice they ever gave me and I took it in 4-5 times), and I highly doubt that'll fix the issue, but I want to avoid that anyway since I think restoring it so many times just made my computer even worse than it already was.

So my my question is has anyone else had this issue, and do you know any possible solutions if so? And also, do these frequent freezes/crashes and/or factory restores damage my computer in the long run? I'd really be upset if the issue was resolved but in a couple of years my computer shuts down because of the garbage I'm dealing with now. I just downloaded the latest version of El Capitan, so it's possible that patch may have fixed it, and I will update if it's still crashing. But I'm being proactive and asking for help in the community because in my seven years of Apple service, Apple themselves have literally never ever helped me.

TL;DR My computer's about four months old and it freezes and crashes a few times a week, usually when using downloaded software. Is there a solution? And even if this is resolved, will these crashes and potential factory restores damage my computer in the long run?