When you purchase weapons, on the same screen where you choose how many of them you buy there should also just be an option to choose what upgrade level you want to buy them at (assuming you’ve already unlocked the upgrades). So you’d click “Purchase,” the next to the number of weapons you’re buying you can also just toggle the upgrade level, shown as stars. Would be make for a much cleaner experience when outfitting a squad with new guns.
On that matter, when you’re upgrading weapons you already have currently it only checks for weapons that are in the reserve for letting you upgrade multiple weapons at once. It should also let you upgrade weapons that are equipped in the current squad. If you had 4 Assaulters with unupgraded SMGs, then you unlock the upgrades, you shouldn’t have to do each upgrade 12 separate times (3x for each Assaulter), but just once for the entire squad’s equipped SMGs. Also rather than forcing you to just do one upgrade at a time, it should let you buy all available upgrades at the same time.