I just went and checked the leads on my tender and noticed that the positive lead from the charger is insulated, neg is exposed.
That means the charging cable from the battery has an exposed positive lead which can be dangerous if the cap is missing. Exposed negative leads on the bike are not really serious. You need to ensure that the insulating cap is always installed on the charging lead from the battery to prevent this from happening again.
The smoke you saw was probably from the tender lead. The battery is able to pump out over 200 amps when this happens arc welding things together. If the positive post portion of the extension isn't melted, I'd look really close at the positive post on the battery to see if it wasn't damaged internally or melted. Pull all the wires off both battery posts and check for arcing, melting etc.
Make sure you don't have your face close to the battery when doing this because these batteries will explode when grounded out like this.