It's fair to say that the BBC are going to be under huge amounts of scrutiny for the forthcoming EU referendum. They've already been derided for perceived lack of impartiality, having already been found to have received huge amounts of money from the EU (millions) and also for their frequent interchanging of the term 'EU' with the word 'Europe' at seemingly every opportunity.
The latter issue is a huge irritation not just because it's a blatant mistake but because that simple switching has a huge impact on perception over the referendum. People generally like Europe as a beautiful and diverse continent but couldn't give a flying fig about the self appointed technocrats masterminding their federalist dreams from Brussels and Strasbourg. Yet this isn't the BBC's issue alone and new reporting in general has been slack all round.
But when it comes to the money, the BBC appear to be on less stable ground. Only back in February 2014, Miles Goslett from The Spectator ran a story detailing how a Freedom Of Information (FOI) request to the BBC uncovered millions had been received in EU funding.
See here: http://blogs.new.spectator.co.uk/2014/02/the-millions-in-eu-funding-the-bbc-tried-to-hide/
So here we are a year and a half later and The Telegraph are running a story about BBC Media Action (BBC claim this is an independent charity) apparently received over £9 million in order to "deliver the EU’s “European Neighbourhood Policy”.
You can read the full story here: http://www.telegraph.co.uk/news/newstopics/eureferendum/11953172/EU-referendum-bias-row-after-EU-pays-BBC-charity-9m.html
Regardless as to how the BBC try to extricate themselves from this perception of money fuelled sock-puppetry, their reputation for impartiality will have taken yet another hammer blow after this.