We have the same problem with uploading our app to App Store Connect. Here are the main points.
We see this error:
ERROR ITMS-90164: "Invalid Code Signing Entitlements. The entitlements in your app bundle signature do not match the ones that are contained in the provisioning profile. According to the provisioning profile, the bundle contains a key value that is not allowed: '[ ]' for the key 'com.apple.developer.healthkit.access' in 'Payload/XXXX.app/XXXX'." The com.apple.developer.healthkit.access array includes health-records in our provisioning profile, but not the com.apple.developer.healthkit.access array in the app bundle's entitlements file
Removing the existing provisioning profile and creating a new provisioning profile doesn't fix the problem
Adding health-records to the array in the entitlements fixes the problem and we may upload the app successfully, but this doesn't solve the problem, since we don't need the access to the Clinical Health Records API the health-records entry allows