Do some more testing. Drive the car on a road for a short distance. Does the battery sustain damage then?
Also be sure to install the battery somewhere in the back, or at least not front where it’s prone to collision damage.
I’ve never heard of engines or alternators damaging the battery in the game in all my time of playing. I’m sure it’s not that. Whatever is damaging your battery, it’s either a bug or something keeps hitting your battery. You always get a message if your car collides with something, so keep an eye on that too.