Did I miss something about G.U.N?

After Team Sonic are attacked at the Chao Garden, they flee the scene to avoid confrontation with G.U.N with Tails questioning why they'd flee when they're on the same team to which Sonic replies that something feels fishy. This leads Rockwell to believe Team Sonic betrayed them in some way.

For the heist on G.U.N Rockwell is now treated as almost a secondary antagonist and I'm unsure on the motives Team Sonic have for breaking in and stealing the other keycard. G.U.N technically had the situation under control and had caught both Robotniks until Knuckles messed it up.

Other than "plot" reasons, was there a scrapped storyline where Rockwell had ulterior motives or something?