Shoulder complaints are common with the low bar technique. You want to first address the obvious things:
- Are your wrists badly bent under the bar?
- What is your hand position with respect to the bar?
- Are you putting the bar too low?
- Are you trying to get your elbows too high?
- Do you have a foam roller and are you using it?
I've had some shoulder/elbow pain at various times through my training. I generally found that foam rolling/lacrosse balls have helped with sore spots. I also found that over time, I adapted to the stress. I have made some grip adjustments along the way, but low bar generally does not bother me any longer.
Keep an eye on it. Do the necessary maintenance. If it gets worse, get a massage and tweak your hand positioning as needed. If it is crippling you, take a break and/or try high bar squats.