I don't understand why not. Did it not have a bar code? Maybe it was not a suitably informative bar code (e.g. maybe your BP bar code only contained the PNR and not name, flight number, date...just speculating.)

Or did they not use scanners but bureaucratically insisted on the confirmation and not BP?

Are all the LH passengers (see post from malgudi just above) going to miss their flights?

Joking aside, I assume this is just teething troubles. Things will settle down.