I had the same problem starting with the very first level, I couldn't sometimes hit the bikers point blank in the early barracks, and I have it again, just like you, in level 3 (El Paso), espacially when you trudge along the rapids during the latter part of the level, I would aim for a Billy Ray (the fat barefoot guys with overalls, a trucker hat and a scattergun) across, shoot the crossbow, it would run full left to the point on exploding on the wall behind me, and even hitscan weapons like the Casull or scattergun would prove useless.
Also had this indoors under the attic of a house in El Paso (which ony I don't remember, maybe the ruined saloon next to the general store) where my crossbow bolts would spin around like they pointed left while going straight away, but still missing targets.
I can only take three wild guesses, one I judge invalid right off the bat, and one I find dubious given my experiences with Blood, Shadow Warrior and Duke Nukem 3D:
1. The game was not properly coded and sometimes while interpreting vertices and tiles on portions of the maps simply could not register the bullet direction right, because that and enemy pathfinding are handled by the same, or similar scripts.
2. It may have something to do with the resolution and the rendering options (although I have no idea how you set those up on a mac, and the stretching and aspect ratio options unless you're playing at full resolution with no stretch and only the basic render (Overlay) (1600x1200, which results in a gigantic letterbox ruining you field of view on a 1920x1080 monitor), the game has a problem between what is displayed and what you're actually doing, but it seems a bit far-fetched.
3. The game does not run properly on DOSBox because something something not 100% accurate emulation I guess (I am not a programmer so I do not know the intricate details between functional and accurate emulation)?
Frankly I disqualify option #3 right off the bat, because why only ONE game so far would turn up like this in my library, and I have serious doubts about option 2 because that would happen all the time, including close quarter encounters, but it only happens sometimes, and in my case, the accuracy problems depended on which side of the river I was on, from the left side the game would interpret Leonard as ailming way to his left (to the point of shooting behind his back when facing straight right), and on the right side it would be okay.
And just as roxoevil said, I also have witnessed a lot of Billy Rays spinning aimlessly trying to find where to look, which would make them intangible for the hitscan weapons (but -if I remember correctly, not to splash damage, so shooting the ground with the crossbow instead of aiming for a direct hit could damage them -then again maybe it was only when they would stop trying to move -so wonky aiming and bad pathfinding). Same stuff applied to the bikers.
Thus it seems to me they messed up something during development and the scripts screw up on large maps because the game does not understand the character opsition (maybe due to vertex orientation or such, I am saying this because I remember from my time learning to use a DooM map editor (and never producing anything whatsoever out of it) that to make a staircase you had to set the vertex orientation so that each step would be "looking" in a certains direction, I don't know how the Build works in this regard, but it's the only plausible explanation I can come up with.
Then again, it could be the extra display setings added by GOG who screw up something during gameplay on open map portions, but that would be weird for only one game.
TL;DR: Rides Again is probably lazily coded and some areas with unchecked scripting confuse the hell out of the engine, which forgets how to aim and how to handle enemy pathfinding.
So in those times I wonder if I should not play with cheats to lessen the frustration...
Or find a way to kill the "auto-aim" feature, because thet might be what confuses the game?
EXTRA:
Apparently this happened on the original (according to the poster who waid it sucked). Maybe, according to the last post on the page, it is linked to DOSBox failing to read something off the SETUP.INI file ?