This sort of thread is very attractive to pricing managers who are on the prowl to close down anomalies

So.... I've sent you a PM
There are numerous reasons why it can occur.
But, when it does occur, some pricing managers will do anything they can to try to "eliminate" the "anomalies". In some cases they are unsuccessful, but where they are successful, it is usually done by increasing the cost of the cheaper ticket, to match the more expensive ticket.
Here are some examples:
- Some Train Operating Companies (TOCs) are expensive, such as East Midlands Trains or CrossCountry. They increase the price of tickets that they set by as much as they can get away with. Other companies will price the tickets they set the fare for at a more reasonable rate. For example, Oxford to Inverness (not via London) is very expensive, as it is set by Cross Country, but Oxford is on a permitted route from London to Inverness, so you can buy a ticket from London, which is set by East Coast.
- Some Train Operating Companies (TOCs) have huge price differentials for peak/off peak travel, while others do not. In some cases of travelling off-peak, buying a ticket priced by a TOC with a large differential, can reduce the cost of a journey. In other cases of travelling at peak time, buying a ticket priced by a TOC with no differential, can reduce the cost. For example, for travel with TPE at peak times, find a fare for a longer journey priced by Northern. PRIV holders in particular should look for fares set by Northern.
- Sometimes there are routeing anomalies, such as when a ticket from Newcastle to Carlisle was valid via Leeds & Manchester. Forum member Squeaky did this journey, but the Routeing Guide was changed a few months later. (see:A handy ticket for Northerners)
- Sometimes it's because the pricing manager has forgotten to increase a particular fare. There is an example in the Bristol area, that is particularly good (I will not mention it here, to avoid giving it more publicity, as the more publicity it is given, the more chance there is of it being 'fixed'!)
- Sometimes it's because of clustering. In order to keep the database a reasonable size, stations are often clustered, the easiest way to see this in action is to look at brfares.com and tick "expert mode", which shows all the stations in the origin & destination clusters.
- Sometimes it's because of rules regarding the Network Area. For example the holders of certain Railcards cannot obtain a discount for travel wholly within this area, at a time that an 'off peak' fare is not valid. In some cases it can be cheaper to buy a ticket valid for travel beyond the Network Area.