Yes, this can happen. The fare for the rebooked routing was probably higher than the one you originally booked. You wouldn't be charged for this fare difference because the change was involuntary.

This happened to me recently. I did a buy-up to Polaris US-Europe. An overnight thunderstorm delayed my morning flight and would have caused a missed connection. When I called the 1K desk to find a different route, the agent put me in the only available fare bucket (C or D, I think), which generated an extra 2500 PQPs and 27,500 RDMs.