One of my players has pointed out to me that my players are currently getting a bonus when dual wielding because DnD beyond adds the strenght/dex bonus to damage when hitting with the off hand weapon. 

Is there some setting or change i need to make to stop this being auto applied whenever a player rolls for damage on the off hand attack, or do I need to remember to manually remove it each time? 

There is a checkbox hidden in the 'customize' option when you select a weapon on your character sheet: "Dual Wield".

When you check that box, the weapon moves to the 'bonus actions' section on the Actions tab, and no longer shows the STR/DEX bonus to damage.

What happens though when you actually have the Dual Wielder feat? That modifier should be there again but it doesn’t seem to be working that way. 

Quote from Deep_Cut_Films >>

What happens though when you actually have the Dual Wielder feat? That modifier should be there again but it doesn’t seem to be working that way. 

 The feat says nothing about adding your damage bonus modifier to the bonus action attack.

You need the Two-Weapon Fighting Style to add your modifier to the damage roll, not the Dual Wielder feat.