If it's an issue of security status, you might need to disable the System Integrity Protection.
When I upgraded to El Capitan SIP created such Terminal pain until someone posted about it online.
Simple instructions:
1. Boot in recovery mode (restart and press command+R when the computer is starting up)
2. Open terminal when recovery mode is up
3. Type in: csrutil disable
4. Reboot normally
5. Do what you need to do, change what you need to change
6. Repeat 1-3 except type: csrutil enable
A more comprehensive set of instructions are here:
http://superuser.com/a/981163/525367
Although it's a pain to deal with, it's important that you reenable SIP.
Remember these steps in the future whenever you run into terminal issues that didn't occur before, it's highly likely that the System Integrity Protection is to blame.
If it's not a system security issue, then I'm as stumped as you (I'm new to ImageMagick and I'm having my own issues cropping an image and getting an error...)