It's only you for now I guess.
Maybe it's a bug issue with your phone firmware since you tested the lower version better to stay with that version until they release a new firmware for your phone.
I am using mycelium for almost 2 years and never encounter any problem with scanning QR code or anything.
Do you have a backup of your coinomi wallet?
Try to hard reset your phone after you flash your phone into the latest firmware and install the coinomi and mycelium wallet and try again if the issue persists it is not a phone problem its a firmware bug.
How about the other firmware which is 5.0.2 just found from XDA-developers.
Check the source here
https://forum.xda-developers.com/oneplus-3t/how-to/firmware-modem-collection-flashable-zips-t3565535If the 5.0.2 didn't work better to stay at the 5.0 version just to keep your qr code scanner work.
I am 99% certain it's a firmware bug.
I think the problem is, and for it to happen to you 3 things have to be in place:
1) You own a OnePlus 3T
2) You use Mycelium wallet
3) You run the latest and greatest beta firmware as soon as OnePlus releases it.
I am guessing that it's a very small group of people.
However, I did think that it would be more then just me talking about it here.
Through the OnePlus forums I found someone close to where I work with a 3T, who is running the beta. He does not use bitcoin but did agree to let me install mycelium to check on his phone sometime next week. Just to eliminate some odd hardware issue on my phone.
I'll also check out the XDA firmware you posted.
-Dave