I wouldn't say poor coaching, but poor time management and goal-line play calling.
The question on bad time management is was it Gibbs (getting the play in late/wrong personnel) or Brunnel taking too long in the huddle? Either way, they really need to work on it.
The 1st and goal from the 1 yard line: Not necessarily the plays called (punching it in), but the bunched up formation. Kinda like Madden was saying, if they had spread it out some, it would have spread out the defense and given them more of a chance for a real push.
As for the refs, yeah they blew quite a few calls, the biggest being the bad call on Harris in the end zone and the non-call when Gardner was pulled down in the end zone. But, right or wrong, the "human factor" is a big (and important) part of football, so I'm very hesitant to blame the loss on the refs. That was a very good heads-up play for Brunnel hurrying up to the next play when he knew Portis should have be called down short of the 1st down....