Thanks for the quick and informative reply Mark, turns out this is happening because many of my inbound routes have "presence_id" hardcoded to the domain they were created on and this number/route must have been created in domain B then moved to domain A without a close review of the dialplans.
For others who may be curious, I studied the CDR as Mark suggested and noticed in the "Application Log" portion of the CDR very early on the presence ID is using the wrong domain name. The "Destination" settings for that number looked okay, but in "Inbound Routes" I noticed that presence ID is hardcoded to instead of using the ${domain_name} variable. I quick spot check and I found that not all my inbound routes have this entry, but those that do are hardcoding the domain name rather than using a variable.
Thanks again Mark and kudos on an amazing platform (maintainability is everything, verbose logging and easy access to it makes life easier for those supporting systems, I just didn't give enough attention in my first review of available information).