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[Gabe Kade]

Everyone suffers from it, thought I doubt most have noticed.
I have Xbox360 version of the game. 
As you progress in the game, you find/buy/develop upgrades to the defenses for both yourself, and your squad/team. If you where to continue playing the game, no bonuses other than character specific weapons will be present in the game. 
The only way to apply these bonuses to your squad is to save after landing/beginning a mission, and then reload that save. 
The best example of this is Legion. If you land on a planet from the Normandy, with full upgrades, Legion has beginning shields and beginning HP (go to squad to check). If you save then reload the mission, Legion will have full upgrades. 
This applies to Mordin's Omnitool, and Jack's implants, all defense systems for all squad/team members, and all damage modifiers i.e. "Pulsar Thingamajig" for shotguns.
This does not apply to any character specific weapons i.e. Legion's Widow rifle, or Grunt's Claymore Shotgun. 

[Xerxes52]

Indeed. It also affects armor bonuses.



I always use the off-hand ammo pack for a few more rounds, and I notice that I frequently will not get the bonus ammo cap.



Saving + Reloading usually fixes it.