Improper Rack Position on Front Squats?

I only train olympic lifts on occasion (I’m primarily a powerlifer), but I alternate between cycles of back and front squats while following 5/3/1 for powerlifting.

I use a clean grip when training front squats, racking the bar on my delts/in the groove of my clavicle and keeping my elbows up. When first training this movement heavy, I noticed my entire collarbone would be sore the next day. However, as I’ve adapted to the rack position, I now notice that only my right delt/collarbone side is bruising.

Does this indicate an imbalanced positioning of the bar?

This indicates an imbalance in your shoulder mobility. You may be able to get your arms up to rack the bar, but the ability of your shoulder to maintain position in the joint while racking the bar.