The Blue Jays challenged a safe call at first base in the fourth inning, after Mark Buehrle appeared to pick Wil Myers off. The umpires reviewed the play and eventually the call was overturned, so Myers was called out. Here's the play:
However, Gibbons did not challenge the play until Buehrle was back on the mound and Yunel Escobar, the next batter, was in the batter's box. Here is what the rules say about the necessary timing for a challenge (emphasis mine):
Except as otherwise set forth in Sections II.D.2-4 below, to be timely, a Manager must exercise his challenge (by verbal communication to the appropriate Umpire), or the Crew Chief must initiate Replay Review (if applicable pursuant to Section II.C above) before the commencement of the next play or pitch. Such challenge or request will be considered timely only if the Umpire acknowledges that communication within the time period specified above. For purposes of these Regulations, the next "play" shall commence when the pitcher is on the rubber preparing to start his delivery and the batter has entered the batter's box (unless the defensive team initiates an appeal play in which case any call made during the play prior to the appeal still may be subject to Replay Review). A challenge to a play that ends the game must be invoked immediately upon the conclusion of the play, and both Clubs shall remain in their dugouts until the Replay Official issues his decision. No substitutions or pitching changes may take place while the Umpires are in the process of invoking Replay Review.
Based on the bold text, the challenge was late because Buehrle was on the rubber and Escobar was in the box. It appears manager Joe Maddon and the Rays have a strong case with their protest.
The first protest in nearly 30 years was upheld just this week, when MLB ruled the umpires improperly called a Giants-Cubs game early due to unplayable field conditions. The grounds crew had trouble getting the tarp on the field and the infield was soaked. The two teams resumed the game later in the series.
The Rays lost the game on Jose Reyes's tenth inning walk-off single, so they won't be dropping the protest. MLB will review the play and determine if the challenge call was late, which is appears it was. The league can uphold the protest and have the teams resume the game from the point of the challenge at a later date.