The charity commission have limited resources and 160,000+ charities to manage - the WBTS being just one of those. That's a unbelievably huge task and they have set up a framework of transparency to ensure demonstration of public benefit. In terms of investigations funding terrorism is a key area of their focus as well as the issue that seems to be a clear weak point for JW's - child safeguarding. They are investigating a case (that went to court and been covered in the national media and somewhere on JWN) so they take issues seriously.
Until they do something specifically illegal where their finances are concerned (in the UK they tend to have a more simple model of paying for bethel UK, printing operations with some funds going to USA via transfer pricing which is acceptable and payments for some overseas activities in Africa) it's more likely their medical stance on blood or historic child safeguarding policies that will create issues.
The area that I've seen questioned repeatedly on JWN is that of public benefit - many being outraged at how JW's actually deliver public benefit? But for as long as religions are allowed a tax exempt status in the UK - then JW's fall quite squarely into that category. I understand it can be very frustrating given how damaging the WBTS is to youth prospects (education being damned), shunning, health, mental health... need I say more?
mmxiv