That's a curious message since InDesign CS6 only runs on Intel Macs, and not PowerPC computers which haven't been around for years.
Also, there's no support for CS6 on El Capitan. It may install and run, or it may not.
HOW did you install it? Via TimeMachine or migration or backup or from the original installer?
I got this error
El Capitan 10.11.6
Adobe CC 2015.5 suite installed
Annoying client still uses Id CS6 and cant share work with them
tried to install Id CS6 for this guy under his account, it installs then when you try run it you get the powerPC error
I logged into my admin account and it installed and worked -phew-
I have another 10.11.6 machine here which i couldnt install it on at all