Sometimes when you grab a new gun during a mission, it gets submitted to the research department.
You lose the gun, but get a head start on researching it.
Sometimes it doesn't get submitted. You just keep the gun, but can't reload it until you have researched it.

Does anyone know what influences whether it gets submitted or not?

Its suppossed to be the first of every new weapon you do not yet own. Subsequent finds should remain in your inventory, researched or not.

But this is not the case.
In the first mission, I grab an uzi off a guard.
So far, I've run this mission 11 times.
It has been submitted 3 times.
This is how I discovered you cannot reload it until you research it yourself.
It also appears (Though I only have observational evidence at this point) that if you do not submit the first weapon that you find, you will never submit that weapon.