The excuse I often hear on GNER for no reservations is "a reduced turnaround at King's Cross".
What annoys me then is when there is one HST at King's Cross. Another arrives in, late. Two HST's are due out, one in 5 minutes, one in 50 minutes. The HST that's come in late is diagrammed to leave in 5, the one that's been sat there for ages in 50. Yet GNER seem to never swap the sets around - rather attempt a quick turnaround, so no reservations, no catering, and a late departure!
Anyhow - sometimes in periods of chronic service disruption, I think reservations are declared invalid. I've not heard of any TOCs charging for reservations.