I have an order that was both shipped on time and that had a tracking number. For some reason, Etsy marked it as having no tracking number and being shipped late. This is very frustrating. I tried the chat function for help but that was useless.
Did you use Etsy labels? If not, did you upload/enter the tracking number before the final "ship by" date?
Also, if added manually, any slight error can cause it to not be read correctly (that includes something as simple as a space before or after the tracking number).
I've been seeing some orders shipped with tracking numbers and registering with the shipping courier's site but show "No Tracking" or "Pre-Transit" on Etsy when it's "Delivered". I hope it gets fixed soon.