Welcome to the forum.
You have stated Canon 5D footage, but have not listed either your Sequence Settings, or your Export settings. Can you please provide that info, as it might hold the answer?
Have you tried exporting your project with one of the YouTube export presets that are built in to Media Encoder?
YouTube can be a bit flaky with its upload.
Make sure you use a Youtube preset with either CBR or VBR1 if using CC.