Did you ever solve this problem?
I have the same problem.
This has become a known issue with FM Go. There is no fix that I know of as of yet. This only happens with QR codes.
The issue is actually having the camera looking at the QR code when the scan is launched. The work around is telling users to make sure the iOS device is not pointed at a QR code when they initiate the scan script. Then find the QR code and scan it.
This is very easy to test if you have a barcode and a blank sheet of paper. That is what I did.
Users thought this was a horrible bug. They prefered to enter the 4-5 digit number for the code manually rather than deal with the possibility that the app crashes. They prefer CNS over the native Scan even though it is slower. Filemaker has a few bugs that disrupt user workflow and I do not see why they do not take those things more seriously. Native functions should work perfectly.