Simple solution here is to prevent reloading while you're transitioning to or from any prone stance adjust.
Listed below are all the affected side effects of being able to reload during these transitions, assuming CTRL is the "Stance adjust" modifier key:
In default prone, reloading while transitioning:
- Up (CTRL - W - R) - Reload longer, reverts to central
- Down (CTRL - S - R) - Reload longer, reverts to central
- Left (CTRL - A - R) - This is the repro - Reload shorter, reverts to central
- Right (CTRL - D - R) - Reload shorter, reverts to central
In upper prone, reload while transitioning:
- Down (CTRL - S/A/D - R) - Reload longer
In lower prone, reload while transitioning:
- Up (CTRL - W/S/A/D - R) - Reload longer
In left prone, reload while transitioning:
- Right (CTRL - W/S/A/D - R) - Reload shorter
In right prone, reload while transitioning:
- Left (CTRL - W/S/A/D - R) - Reload shorter
Also of note is that when you are in any prone adjust stances, holding CTRL then initiating a reload you will revert to the central stance with all the positive or negative side effects listed above for that stance.