I have not experienced the problem.
The QR Code reader one uses can have a significant impact on reading the QR Code, especially as the size decreases and the quality of printing. I would suggest trying a different reader and see if the problem persists. If it does, upload a PDF with a code that does not read to dropbox.com and I would be happy to print it and try. If it is sitting on a background of any type, make sure it is in the PDF as well.
Thank you for replying. We have tried it using a different QR code reader and it does the same thing. It's very strange as it doesn't make sense that it would work in Indesign and also if you save it as a jpg it's still readable but as a pdf it doesn't scan. I had previously created the QR code online using a website and placed it into Indesign and that worked when it was saved out as a pdf but it created a white box around it and I prefer just the code with no background. My colleague discovered we can create one in Indesign in whatever colour which is great but am stumped by it not being readable in a pdf. I'm going to try and do the same in Illustrator and see if that works, if not I will send it over to you.
Thank you very much.