My invisalign is for after my braces to keep them, however I found that the bulkiness of my invisalign causes my jaw to sit more open while I wear them. Though I’m not sure if anyone had experienced this, it makes me avoid wearing my invisalign since even after I remove them from my jaw still feels sore. The aching is more of a minor lingering irritability than a pain; it almost seems like you have a minor headache.
Ever since I started using Invisalign, my jaws have been sore. It produces persistent strain in that area and makes me clench.
TMJ sounds like it. Are you a clencher or grinder?
By the way, Invisalign has little to do with your retainer. Speak with your orthodontist if the problem continues.