Similarly experience on Premiere Pro with unexpected crashes that will rendered the Macbook Pro 15inch 2016 useless. Same symptom with Premiere Pro, the computer will become unresponsive and computer's screen flashing with checkered/blocky pattern. I thought it was an isolate issue with Premiere Pro but now I can confirm After Effects is getting the same treatment on my new Macbook Pro 15inch 2016.
To put you in context I have been using After Effects for work vaguely over a month now. I work on weekday, and every single day I used After Effects to do project ranging from minor to major project. In total I can confidently say that I used After Effects for 30 days and this is the only time I have encountered the infamous flashy checkered pattern on my screen. Premiere Pro will usually crashes on average 30 minutes from the time I opened a project, a painful solution is using Final Cut Pro. Not sure if I could say the same thing for After Effects.
I just want the Adobe community and staff members to be aware of this issue. It's not frequent but this shouldn't happened at all in the first place.
My daughter has reported similar freaking out screens on her brand new MacBook Pro and she was not using any Adobe Products. The screen looked almost exactly the same. This makes me think there is some kind of hardware problem common to both of your machines.
She is taking her machine to the Apple Store for analysis. You might also want to check out this article. There are several reports.