Where did my assault rifle go?

Solution 1:

You can't carry Heavy Weapons around in this game. If you switch from them, you drop them.

When you pick up a Heavy Weapon, it temporarily replaces your current weapon from the weapon select wheel - the reason you couldn't find your Assault Rifle was because you technically still had it as your active weapon.

So you then switched to your pistol, which dropped the Heavy Weapon (on the ground nearby, able to be picked up again).

After this, your Assault Rifle should have been selectable again. Did you only try to switch to the assault rifle while you were carrying the Reaper Blackstar (the Heavy Weapon you found)?

Solution 2:

This seems to be a bug. I've had the same issue and I was only able to get my gun back by loading an earlier save. Otherwise you are forced to finish the mission without your gun.

I've had that more than once but it happens relatively rarely (2-3 times per playthrough) so it's not easily reproducible. Hopefully they will fix that soon.