I recently had the same experience, and I thought we fixed this a while back. I'm pretty sure we did, so I wonder if that fix broke more modern android....

On Fri, Feb 13, 2015 at 3:00 PM, Johnray Fuller <jrfuller@redhat.com> wrote:
On 02/13/2015 03:53 PM, Nathaniel McCallum wrote:
> I recently got a Nexus 6 with the 5.0.1 Lollipop OS. I noticed that
>> when the application activates the camera, the image is upside down--
>> making it hard to orient the phone when capturing the QR code.
>>
>> I am not sure if this is a design choice or a bug, but wanted to
>> call it to the attention of the developers in case it is
>> unintentional.

Done. The bug report is here:

https://fedorahosted.org/freeotp/ticket/57

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Johnray Fuller
Solutions Architect
Red Hat Inc.
jrfuller@redhat.com
c: 917-453-8216
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-Jon Disnard