Actually, you can--but you can't do it inadvertently. You need to:
- Create a basic PNR in your CRS
- Manually add the flights as confirmed outside your CRS (there are a range of "K" codes available)
- Manually select the fare code for the booking
- Issue the ticket
If the airfare was from the tour operator, the agent didn't issue the tickets and the fares used would be based on override ticketing codes.
But let's keep it real: being a travel agent is literally unrewarding. Crap pay. Crap travel benefits compared to 30 years ago. Having to pay thousands of dollars for your entry level training yourself in many parts of the world. The recognition and reward system (irony here) means anyone clever moves up or out. Consumers are getting what they pay for.
You can't issue a ticket without a valid PNR from the airline attached. The issue lies in that AC did not "get" the info from LH, probably due to AC's never ending terrible IT. The TA/Tour Company are really blameless here.