With regards to everyone always having their weapon during those capture scenes, I admit it wouldn't make sense the first time at Shinra HQ. I too came to the conclusion that everyone's weapon was stored right outside the cells and they probably rearmed during the whole "Split into two teams and follow Red XIII" bit. Now a related question, why didn't Shinra at least take whatever materia might have been slotted into those weapons before they stowed it?
The second time the team gets captured by Shinra, this time just Tifa and Barrett, let's see... I can see forgetting to take someone's glove away from them when they've been in a coma for seven days, can't you? Depending on which weapon Tifa has equipped of course, if it was say one of the claw-type gloves it might be hard to miss. As for Barrett, I've noticed around that part of the game he lifts up his real arm and does... something... with his gun-arm while he's talking to Cait Sith and Yuffie, several times. I interpreted the motion as him loading his gun-arm, like they hadn't taken the weapon but they did take the bullets or something (since the unlimited ammo he and Vince seem to have in battles is clearly just a gameplay device it follows he does need ammo, or his gun-arm is just a metal club, and his hands WERE tied until he was rescued). Did anyone else see that?
Not a smooth move. Well, at least they remembered to make up for that in another game further down the series. 
