It's worth understanding there's several different ways of booking an Avis booking which is, in some way, associated with BA:

1) As a flight+car booking - this is done either at time of booking or adding the car after. This creates a voucher on BA.com and you get all the benefits thereof.

2) The other primary one is via avisba.com which is simply a branded booking portal for Avis which provides some benefits (such as a free second driver) and a discount. If you pre-pay on here - you should also get a voucher sent to you from Avis, if you choose to pay at time of rental - it should be charged appropriately at the time.

Now - I've done maybe 30-40 Avis bookings in the last 5 years. Not once have I had an overcharge off a voucher (well - except tiny ones - more in a sec), but most of the time I don't speak to anyone in the rental location as I'm in their preferred system so go straight to the car.

I do, however, frequently get check in receipts that read:

Total $x
Less voucher $y (where y is significantly less than x)
Total to pay $0

e.g. Maths that just doesn't add up.

First time I saw that I panicked but it was fine.

I do occasionally get additional charges thanks to currency movement and rounding. Every so often I get a little 1p charge come through on the card (like once every 5-6 bookings). It's not worth my time and effort to call/email to get it back so I ignore it.