Previously the game was supposed to use the weapon that did the most damage, so maybe with your current strength the bat does more damage than the pistol. I believe the new system allows you to choose the weapon. Have you tried clicking on the bat icon to change to pistol? Another possibility, do you have ammo?
Edit: I confirmed you click on the bat icon and you will have the option to select weapon, which appears to be in alphabetical order, so; Bat, Knife, Pistol.
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