Easy fix - the "red duster"
 

As far as I can tell, our Merchant ships in convoys all carry the Union Jack, whereas they being civilian ships, should I believe, be flying the Red Ensign, known in the Merchant Marine as "The Red Duster", usually a single flag on the stern flagpole.

https://en.wikipedia.org/wiki/Red_Ensign

It's not the end of the world that they're carrying the wrong flag, but it is perhaps an easy fix at some point.

On a similar note, it's traditional for Royal Navy ships, when engaging the enemy, to fly two white Ensigns at different masts. The reason for this is as that lowering your colours in battle was a sign of surrender, and so to mitigate the risk of your colours being lost through a mast being shot away, the 2nd White Ensign was flown. When not in combat, one is, I believe, more usual?