If you've got a common 3-wire harness on the alternator (like almost all cars do) then all someone has to do is disconnect the voltage sense lead (one of those wires) for about 30 seconds and it will fry the diodes and ruin the alternator. This is a common scam for rip-off garages to pull on customers, they disconnect the wire in front of your eyes and then hook up a meter to show you "See, it's dead" and it sure is now.
Then they'll blame it on the battery being bad, so you'll buy both a new battery and a new alternator.
But it simply is a weak point in the common alternator design. Disconnect the voltage sense lead, the alternator says "Oh the battery is so very low, I have to put out full power!" and in doing so, it can burn out in 30 seconds. And damage all the electronics and light bulbs, if they are on.
So...not necessarily a problem caused by the battery connection, although that lead goes from the alternator to a battery, same as the charging lead does.
Boats can be a hard place for electrics and unfortunately it can be a physical PITA to get close enough to make sure all the connections are clean and tight.
FWIW, If you have a "one wire" system, it doesn't have that problem, but there are always other tradeoffs.