@christaewilliam ...
If I am understanding your question correctly, it sounds like you have some pages within your course where you are linking to assignments in the same course? If so, in your "parent" course (where you are copying the assignments from), I would be curious to know if those links to your assignments are really linked properly. For example, in that course, go to your course "Home" page and look at your course URL in your address bar of your browser. What is the CourseID number you see there (no need to tell us here, but just take note of that number) ... which would look like this:
https://SchoolName.instructure.com/courses/123456 where SchoolName is the name of your school and 123456 is the CourseID number
Then, go to your page with the links to your assignments. Hover your mouse over a link to one of your assignments (here I'm assuming it's a Canvas assignment you're linking to). At the bottom of your browser, you should see the URL displayed which is the path to that particular assignment. The CourseID displayed in that URL should match up with the CourseID number that you looked at on your "Home" page. If those two numbers are not the same, then that tells me something has happened recently or in the past...such as where a link may have been copied/pasted from one course to another (something that is not a best practice). There could be other reasons, but this is a common one when people want to link to things they used in past courses.
I know I'm probably making some large assumptions here...especially since I'm unable to see exactly what you're looking at, but maybe this will give you some things to look at for starters. Keep us posted here in the Community...thanks!