Plot hole: The crew makes no attempt to re-board the Enterprise or stop it from leaving the starbase even after they find out there is no danger from the anti-matter.
Plot hole: During evacuation, when Wesley is beamed off the ship, there are room for one more person on the transportation pad. You would think they would like to transport as many people away as fast as possible.
Plot hole: The binars needed two people to upload the data back to their world but they only intended on keeping Riker in the holodeck. Riker is just one person. Picard came into the holodeck purely by accident - even Minuet said this was true. If Picard hadn't been there, Riker could not have uploaded the data on his own and the binars' plan would have failed.
Suggested correction: The Binars only trapped Riker because they thought they might need someone to restore the computer for them, which wouldn't have taken 2 Enterprise crew members. It was the fact that the Binars got to their planet too late that required Picard and Riker to work together. However, the Binars already knew Picard was on the Holodeck before they initiated their plan because when Picard exits his ready room he says he's going to join Riker. Had Picard not done this, certainly the Binars could have kept a 2nd crew member on-board somehow, if needed.