University messed up my fees! Am I liable

My friend enrolled at a Scottish uni to study 3 undergrad x20 credit modules- he was charged £650...

...and passed one module and failed the second.

He’s been told by the uni it will cost him £500 to resit his module...

...and they’ve just realised a year later that he’s not been charged for the second module he did and is due another £650!

Is he liable to pay this considering it wasn’t his fault- it’s a year later...

...and he’s asked others on the same course if they were charged £650 a module and they have only paid once too!

OK. Further confirmation that the £650 was supposed to be per module. (By the way, you don't mean "due". If you're "due" something, then you're scheduled to receive it.)

If he wants to resit the failed module then he will need to pay, yes. If a company makes a mistake and undercharges you, you can try to avoid paying them the difference once they realise, but you can't do so if you want to continue doing business with them. They'll just refuse to deal with you.

When you say "they have only paid once", that doesn't really tell us how much they paid. They could have paid £650 once or £1300 once or £1950 once.