I'm a little tired so I might be reading this wrong. I assume you're saying Alcantara has 11 errors at 2B? I'm confused mainly because baseball ref has him at 9 errors(.966 fielding%) at 2B this year. Either way, over all his time at 2B, Alcantara has 767 chances with only 38 errors or a .950 fielding%. That's pretty decent. Obviously fielding% isn't the end all stat for defense but you're unlikely to find good coverage of defense stats wise in the minors anyways. Either way, it's definitely good enough to play there going forward and possibly good enough as he continues to mature to be a plus there.
As for him in CF, it's either a case of poor foresight or they felt 2B was a better position for him. They obviously have much more information than we do and they are the ones making the plans. So, for them to some how miss the possibility that Baez might need a different position seems far fetched to me. Additionally, OF as I've already mentioned was wide open for prospects as Soler and Almora where the only two high profile OF's and they were ar enough behind Alcantara that it's not a worry of him blocking them. Even if they didn't feel he was a CF, you could have given him reps sooner and slowly transitioned him to a corner OF slot if need be. However, they chose to keep him at 2B until now. That leads me to believe they'd prefer to play him there. Additionally, if he could adequately play CF that'd make him a hell of a lot more valuable as both a player for the cubs and as a trade asset. So, the fact they waited until he was a few months away from the majors to play him there seems frankly odd if that's what ends up happening.
On top of that, when he eventually comes up to the majors you don't want him worrying about his defense. You want him to go out there and focus on hitting. In the case of guys like Upton and Soriano who did move from 2B to OF, Upton didn't play OF in the majors until 2007 which was after he'd seen 95 games and 3 years of near majors development(he was called up in 2004 for 45 games then missed 2005 and split time between AAA and the majors in 2006). In the case of Soriano, he didn't play LF until 2006 which was 8 years after he'd debuted and established himself as a hitter.
If Alcantara plays CF in the majors, I honestly worry he'll have too much new shit going on at once and struggle because of it. I'd much rather see him play the infield where he's played 492 of his 498 games with 441 of those games being at middle infield. In the case of Baez, moving to 3B from SS isn't really a huge transition. So, even though he's not played 3B in the minors I'm not really worried about that. Bryant played some RF in college and his college coach suggested he had Gold Glove potential in RF. However, Alcantara to CF just feels like trying to make shit fit that doesn't. And even if he can play an average CF defensively, you're just going to put yourself in the position to move him again in a few years assuming Almora develops. Almora should be an excellent defensive CF so assuming he hits his way to the majors you'd rather have him there long term. If you stick him at 2B and give him a few years to develop, even if he fails you still have the option to move Baez from 3B to 2B later and allow an opening for someone like Villanueva or Candelario which would allow Bryant to stick in RF.