Were there problems behind the scenes? Tomino has essentially apologized for how that show went, which seems uncharacteristic of him.
That's a bit of a mistranslation of what he said. What Tomino said was that if people had trouble understanding G-Reco and they think it's because he did a bad job directing, then he apologize. Same interview has him saying he likes the show.
There's a lot of stuff about G-Reco that ANN didn't cover. You know it sold more video (Blurays or DVD) than Aldnoah Zero or Cross Ange (by a large margin in Ange's case)? Or how about it being praised by an anime critic in one of Japan's largest newspapers as well as Gen Urobuchi? You know it aired at 2am where it held a ratings average of 1.8% (when late night anime rarely get over 2%), and once it was over it's reruns were given a better timeslot? Heck, Yaraon (who ANN used as a source for the Tomino interview rather than the magazine it was in) polled it's readers and found that out of 500 people, 54% thought G-Reco was the better show over IBO.
The show wasn't this massive failure, it was a decent hit for a late night anime. If anything, this was something Tomino was given full control over because it wasn't expected to sell (he was reportedly very upset over the timeslot). They didn't have faith in him, but he delivered anyway.