If their system comes up with a different delay to what you claimed, for example, they will usually pay what they think it was, even where it is greater than what you claimed.
Or if it is less than you claimed
This has just happened to me - on Saturday I travelled from Sway to Weymouth.
My journey should have been (following the Journey Planner):
Sway (09:26) -> New Milton (09:31)
New Milton (09:45) -> Weymouth (11:05)
What happened was:
Sway (09:32) -> New Milton (09:37)
New Milton (10:22) -> Dorchester South (11:33) (cancelled to Weymouth)
Dorchester South (12:46) -> Weymouth (12:54)
So a full 1:39 delay. (problems at Poole level crossing I understand)
(to be fair, I could have walked to Dorchester West and gone from there (12:12) -> Weymouth (12:24) - but still well over an hour late)
So I put in my claim for 60 minute+ delay. But SWR came back with a 30-59 minute delay. Why?
Well, it transpires that,
if I had ignored the journey planner and travelled to Bournemouth to change, I could have picked up a delayed Bournemouth-Weymouth train there and arrived at Weymouth earlier.
Sway (09:32) -> Bournemouth (09:57)
Bournemouth (10:36) -> Weymouth (11:35).
Now, I wonder if I have a case to appeal there... (it's only an extra £4 or so, but annoying!)
Just to round things off, getting to Weymouth to catch the 16:00 service back, found everything delayed due to a signal failure around Moreton. Got home an hour late - also claimed for that, haven't heard back yet though...