Let me start by saying the obvious - I’m not a doctor, so I cannot diagnose, treat, or otherwise help with any injuries or health conditions.
Your doctor is your teammate when it comes to working around these and she or he can give you guidance as to how to approach this program the right way - to prevent further injury and to aid on your journey to a healthy and happy life revolving around fitness.
I, therefore, recommend that you see your medical provider for any aches and pains, regardless of how minor, to prevent any long-term injury or damage.
There’s no shame in taking a few days off while you heal - a few days to recover is A LOT better than a few months because you didn’t “listen” to your body. Again, we're here for long term results that are sustainable and that compile on each other - when your body "tells you" it needs a break, take it :)