How can I determine if my refund was accurately filed? WheresMyRefund says it was accepted but the transcript says not filed.

It has been nearly 90 days since filing and my IRS transcript says nothing is filed. I've spent nearly 6+ hours on the phone trying to just ask the question to the IRS but they just hang up. Initially my filing was rejected because turbo tax left out a document/question but that was rectified 2 days later and that return was accepted.