|A surprising number of people on banknotes haven't been in DW episodes|
It's not entirely clear what happened - apparently some allegations were made and an internal investigation started and found to be accurate. The BBC doesn't wish to provide further details, understandably, so there's no knowing if the money went missing from the Casualty budget or the Doctor Who one (he worked on twenty episodes from the middle of Series Three to "The Next Doctor", as per his IMDB page, and then moved to Casualty). There was one official comment: “Since Oliver Ager committed these crimes the BBC has reviewed its cash processes and ensured that there is additional oversight to prevent a crime like this from happening again.”
The Wales article says that he was "director of an independent production company called Different Productions Ltd from December 2011 until October 2012, the month he was dismissed by the BBC." Which there aren't any records of online, barring a unit in Buckinghamshire, so it probably wasn't a large-scale proposition.