I have a separate script that signs my embedded frameworks.
This was worked fine form 10.9 - 10.11.
On 10.12 I get a segmentation fault.
codesign --verbose --force --sign "$IDENTITY" "${FRAMEWORKS_LOCATION}/${FRAMEWORK}.framework/Versions/A"
18939 Segmentation fault: 11
Running the command outside of Xcode produces the same result.