Our agency purposely color codes everything. 9mm ammo is issued in a black box and has a nickel case (in addition to having 9mm stamped on the base). our .40 ammo is issued in white boxes and is brass case (in addition to having .40 stamped on the base). Even when we put training wheels on the ammo to help folks out, they find a way to screw it up.
If you make something idiot proof, they will invent a better idiot.
Side note, DHS may well get a new gun in the next few years. I was told by some folks who are more in the know than me, that a Glock .40 would never get adopted. Not because the .40 Glocks have never run well with our ammo (and it has not), but because the chances of cross pollination between .40 and 9mm goes up exponentially if the mags and guns look exactly alike and the mags interchange. Which is why out Sigs are .40 and our Glocks are 9mm. that way, ammo may get in the wrong mag, but the wrong mags wont fit in the wrong gun... Is that a true management decision? I don't know, but it sounds entirely plausible.
That way, the 3000+ agents who bought a personal purchase G26 or 17 wont have to ditch them if we issued a G27/22 combo.