Their was a little puddle next to the battery and also directly under the battery their is a whole with a big water stain around it. Can any one give me some insight on my problem?

The battery should be sat in a plastic battery tray presumably to catch any battery leakage. The MX5 ships with a special jel battery(similar to a motor bike but much bigger) connected to plastic tubing at the top so it can vent outside the boot which unlike the bonnet at the front has no natural ventilation. I may be wrong but it sounds like the battery has been changed for a lead acid one at some time & which may have a cracked casing which is leaking or the cells overfilled causing corrosion

^ true, most of the time people dont want to replace the sealed battery because of the cost (180) versus (60) but the non sealed battery can corrode and cause issues with wiring and other parts of the car.