I did read your post and I'm not saying you're doing this (since you explicitly said you're not), but it is possible on an S+ machine to sneak an extra coin in. This is typically done by dropping the final coin for the maximum bet and an extra coin into the machine in very quick succession, before the lockout coil has a chance to engage. When that happens, the machine will allow you to spin the reels with your max bet wager, and then will pay out one coin from the hopper to pay the player back for the extra coin that was accepted.
If you are absolutely, positively not inserting an extra coin, you'll need to investigate why the machine thinks that you are.
Note that it's very difficult to fool the machine into thinking that a coin was inserted when it wasn't, so I'm not sure what to suggest other than cleaning your coin-in optics, and ensuring that the encoder (the plastic piece in the coin-in optics that forces the inserted coin to pass by the optics correctly) is the correct size for the coins you're using.