You don't pay fees when you don't win the item! If your snipe was beaten then you won manually then you shouldn't pay fees IMHO - click on HELP and ask for a refund!
Without knowing auction numbers or specific times then it's impossible to guess at a reason. As to it being a malfunction well AS adjusts lead times to suit network/server loads at busy times - could this be what happened here? (and every Sunday evening???!)
R2