Are you aware of any of these 'anomalous' itineraries that have actually been challenged by a TOC during the journey, - and has the traveller been able to get recompense from Trainline?
If the passenger was travelling in accordance with the itinerary, the TOC is
not allowed to charge the customer. The itinerary is evidence of a contract; if it's been issued incorrectly then there are internal procedures to handle this which TOC staff should be following. So in this case, the customer should get recompense from Trainline.
Most of the bugs
@robbeech refers to have recently been fixed. They started appearing in early 2018. See
https://www.railforums.co.uk/thread...orden-to-hebden-bridge-via-accrington.163469/ for a good example of the most spectacular that was reported by
@ForTheLoveOf (and very quickly correctly analysed by
@Starmill)
Easements are perhaps the hardest thing to get right. Some easements are encoded incorrectly too.
There are numerous other things that can go wrong but it's best that I don't go into detail here. Suffice to say the Worldline (Atos) WebTIS sites can have the most spectacular bugs; far more so than Trainline, and several interesting ones remain to this day. But even SilverRail, who are RDG's supplier for National Rail Enquiries, have bugs of their own. No-one is perfect. But some implementations are better than others.
Most suspected bugs tend to not actually bugs in the journey planner at all, but data issues caused by the TOCs themselves.
Occasionally I have found cheaper fares on Trainline; I usually use TPE because I get Nectar points, but occasionally I can beat their prices using Trainline.
If the itinerary is identical, and if both sites support the same fares, the price should be the same. There may be some obscure reasons why not.
If anyone is interested in learning more, feel free to put your name down for one of our free
fares workshops.