Hi, I am adding an expense payment (through the company card) of 25.00 but with the VAT extracted it comes to 24.99 so it will not reconcile with the bank transaction.

Yep, right at the bottom.
If you have a big gap as in you invoiced 100 and they paid 90, then you'll need to create a credit note.
To do this simply click on the invoice for 100 and you'll see credit note in the menu on the right, follow the workflow and we'll manage all the crazy accounting stuff.
You're only allowed about 1€ adjustment by law.
Hope that helps.

Pete