I believe the new CBA is awful and this situation is just one example of the clusterf*** they created. That said, I'm sympathetic to the Pirates situation. Yes they failed to sign their pick, but they offered Appel way over slot, more than a million over slot, and he still didn't sign.
The CBA hurt the Pirates, hurts all rebuilding teams and hurts the players in the draft. The Pirates offered over slot, but with the new hard cap on bonuses you can't pour all your resources into a single player so they were handcuffed by the CBA. Rebuilding teams can no longer pour unlimited resources into the draft, making it harder to infuse talent into the system. From 2007 to 2011 the Nats spent more than $50 million on draft bonuses, including spending more than $18 million in a single draft. That is no longer possible with the hard cap. Finally, Appel would have been a consensus number one based on talent, but he dropped precisely because of signability questions. A year earlier the Pirates could have given him $8 million and proceeded with the rest of their draft, but the Pirates entire bonus pool was $6.5 million and even with that they still offered him $3.8 million.
So the Pirates, all the teams that picked ahead of them and passed on Appel, the Mets, Appel and every other super talented future draftee all get sc.rewed because of the abomination that is the new CBA.