This was actually posted on the BBC website last week (and also here on the forum in the original thread about this story) and their article has a lot more information:
http://www.bbc.co.uk/news/uk-scotland-south-scotland-24897643What actually happened was that he was still on a work visa, but he applied for ILR using form SET(M) instead of SET(O).
So, I don't actually think it was that they thought his marriage wasn't legit, it was that he wasn't eligible to apply for ILR based on his marriage in the first place, because he never switched to FLR(M). Therefore they were correct to refuse his visa because he applied for the wrong one.
If he had applied using the correct form (SET(O)), then his ILR would probably have been granted with no problems.
Or if he had switched to the settlement path by applying for an FLR(M) when he got married, then he could have applied for ILR years ago and already gained citizenship (since he's been married to her for nearly 5 years) instead of spending all that time on work visas and Tier 2 visas.