They were also heavily into licensing. Depending on the agreement (which would be either a % of sales, an up-front fee, or both), they were probably in for 5%-20% of revenue. Given that some of these titles clearly underperformed, that budgeted 5%-20% was probably more like 15%-40%. Combine that with the 30% the online stores were taking, and they're left with a much smaller percentage of revenue than they may have anticipated.
As others mentioned, though, I'm not convinced they could home-grow IP. People were interested in the stories of familiar locales and characters. Even still, The Walking Dead was diminishing returns (so is the TV show, though, with ratings substantially down), and neither Batman nor Game of Thrones, two huge licenses, seemed to sell well.