Sure. If you develop a bad cell in one of the batteries or just sultanate the plates, the potential will drop below 12 V. If you have the switch in the "both" position and the engine is turned off or running at idle speed, current will flow for the good battery with the higher potential to the bad battery where the energy will be lost as heat.
Modern computer controlled engines draw about 10 amps or more while they are running. The alternator puts out less than that at idle or slow trolling speeds. So the engine draws the difference from the battery bank. Under those conditions, a bad battery will draw from the good one unless you have a battery isolator.
If an alternator fails, the engine will draw down both batteries. You won't notice a problem until the amp hr storage capacity of the batteries is approached. If both batteries are connected, once the engine starts to misfire, you are screwed. With an isolator or a battery combiner, the second battery will be protected. After switching to the good battery, you can run for up to an hour off of the battery (depending on the reserve capacity rating and battery condition) despite the dead alternator.
If an alternator fails, the tachometer stops working. You should head for shore immediately if that ever happens. Radio your situation to the CG or other responsible party in case you batteries fail before you get back.