This isn't terribly surprising, as it has been known for some time that the MLBPA and some large-market owners have been displeased with the way the A's have used the revenue sharing dollars that they've been receiving. A team doesn't have to plow it directly back into the major-league payroll necessarily, but it must in some way put it toward improving the product (increasing scouting staff, advancing in-house technologies, making capital improvements, etc.). Presumably, the A's weren't doing that to the satisfaction of certain vested parties.
In a feature that did not change with the most recent CBA in 2012, teams can also earn compensation for unsigned picks from the previous year's draft. If a team doesn't sign a first or second round pick, they will get to pick at the same slot plus one the following year. For example, if the team with the #5 pick does not sign that player, they would have the #6 pick the following year. The regular draft order would continue around those picks. For compensation for not signing a third round pick, teams would get a pick in a supplemental round between the third and fourth rounds. If a team fails to sign a player with one of these compensated picks, there is no compensation the following year.