They have decided there is no problem, based on previous court rulings in Brazil, and submitted the paperwork as early as possible, 1/1/2017.
The FA has to check everything, and they are in the process of making sure everything is correct, a process which should only take a day or so, but has been drawn out to a couple of weeks because of the messiness on the Brazilian side.
That's not the club's fault, nor is there anything they can do except give the FA what they've got. The FA probably can't make it go much faster as they'll have to go through the court proceedings in Brazil and/or speak to lawyers over there and Palmeiras.
The last point is just rubbish, and reflective of the embarrassing neediness of fans these days. Pep explained it was a delay between the FA and papers in his press conference today.
The last time he was around the media was 4/1/2017 and there was no significant hold up, so why bother explaining a hold up that hadn't existed yet?
And if it's not a major problem, why make it into a big deal by doing some sort of special circumstances announcement.