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Hi @tbailey8121,
We also use Ally at our school. This is a known issue to them and covers all course copies, including course templates, import/export, commons, Copy/Send To, etc.
When we were actually able to get their team on a call, they said that this is a limitation of Canvas (and the IMS Common Cartridge standard more broadly). Basically, the only place Canvas stores alt text for an image is in the Rich Content Editor for a page/discussion/quiz question/etc. The idea, "[Files] Default Alt-Text on Uploaded Images", explains what would need to happen for Ally to work as intended.
Moreover, Canvas doesn't provide a way to fetch where in a course particular files are embedded nor does it provide a way for Ally to store arbitrary metadata (such as descriptive text) on a file. This means that when you fix an image embedded in the RCE, those fixes do not carry over to the file itself in the Files area. Likewise, when you fix a file in the Files area, it is only fixed in the particular course you are working in and won't carry over to future courses.
Also, while Ally does break out Files and WYSIWYG content on the institutional report (available to your school's Canvas admins), it doesn't provide a way to exclude certain problems in certain areas (e.g., exclude images without descriptive text when inside the Files tool) from the score.
The reason Ally counts these files in the Files tool against your course's score is because you can make the Files tool available to students, leading to these accessibility issues.
I hope this helps.