InDesign's QR code generator generates v2.1 VCards, and apparently some newer phones/readers don't read the older phone number format that v2.1 writes.
If are using the standard ID Business Card QR template, if you hover over the QR code that is placed in your document, a pop-up should show the information included.
e.g. v2.1 vCard:
TEL;WORK;VOICE:000-000-0000
v3.0 vCards are written differently, and apparently many newer phones require v3.0 or newer
TEL;type=WORK;type=VOICE:000 000-0000
Outside of looking to a 3rd party QR code generator, you can find online v3.0 vCard generators, and paste that info into ID's QR Code "Plain Text" option.
In the meantime, add your voice to the feature request to update ID's QR code generator! (sorry, I don't have a link at the moment)