Depends on the base fare - the OP says it was fully flexible Y on a route deal. Pure conjecture, but I suspect that at face value, there was some weird problem with ba.com calculating the difference between published Y fare on the route and <lowest available CE bucket for sale at the time to upgrade in to> (what the OP was quoted) and <route deal Y fare> and <lowest available CE bucket for sale> (what the OP was actually charged).