A few observations about 12V Batteries.
A 12V battery at rest will read 12.6V to 12.7V (At rest means no charger and nothing drawing current)
A 12V battery at maximum charge rate will show 14.2 to 14.6 depending on battery type
A 12V battery at full charge connected to a charger will show abut 13.2 (float charge)
So from your post if your battery bank was showing 12.5V then it was indicating that that bank was about 80% charged. Maybe you were looking at the house bank? I am not sure of your boat's battery system but you probably have 3 banks? One for house, one for start, and one for thrusters? Maybe you had a dead start battery? Do you have a parallel switch on your boat? If you do then you may have been able to turn on the parallel switch and temporarily use all of your boat's batteries to start your engine. It is also possible that your boat's charging system is not working properly (alternator, solenoid, etc etc). How old are the batteries? Running the fridge for 3 hours would not have caused your start battery to run down unless the parallel switch was turned on but then the voltmeter was showing 12.5 so I'm not sure what was going on.