You applied for extension before the old permit expired, you would have had implied status until the decision was made. As I understand from your posts, you were already out of the country by the time this happened, so it does not appear that you overstayed. Besides, after your work permit expires, you have 90 days to restore.
One thing you could, is just get an immigration medical exam done by a designated medical practitioner in your home country and bring the receipt with you next time. Present it at the border and you will now be in compliance.
If let in, get clarification from the CIC call centre(explain your circumstances, and ask them to forward the information to your email). In your subsequent applications to CIC for similar jobs, you can include a cover letter where you explain that under subsection xyz of the Immigration Act, you are not required to undergo a medical(if this is in fact true).
With CIC you need to decide which is more important to you - being right or doing what's needed to ensure you obtain the desired outcome.