For the example you've given, the link between RID 202508217651923 and 202508227944603 at Petersfield has isCancelled set to true, and the link between 202508217651923 and 202508227944729 at Haslemere is deleted.
I think the original intent of this was to terminate the 2332 Waterloo - Fratton (L51923) at Petersfield at 0050, and run a bus to Portsmouth Harbour (O44536), but this appears to have been changed to terminate at Haslemere at 0033 and run a bus to Portsmouth Harbour (O44730).
I don't have time to look at the entire timeline, but given Darwin is a real-time system, you can likely troubleshoot this yourself by looking at all the messages received for the RIDs concerned, laying them out in order of receipt and working out what data you have received and what you haven't.
Bear in mind that this could be a bug within Darwin due to a lack of strong business rules that require a consistent state of the timetable.
Peter