Just a few things from the article:
They're running out of money. (That's nothing a few more ships for sale can't solve 
)
Cult-leader Chris orders them to make game-defining changes on a daily basis that fucks up everything for weeks. (It's Chris' world after all, you're just living in it 
)
Besides just the main game and Squadron 42, they also have a third game (medieval fantasy) in development that uses the backer's funds as well. 
I remember clowning on Hello Games at the time, but they really managed to turn things around. They basically showed that it's perfectly possible for a developer to actually fix their game, add everything that was previously promised, and to go even further beyond, while releasing new content for free.