The files need to be removed permanently from this site (second stage recycle bin as well) in order to free storage space. Whether you delete files in the end user recycle bin and site collection recycle bin?
Please follow below tips to troubleshooting the issue.
1.Make sure that files are checked in.
2.Make sure that you have the appropriate permission to delete files.
3.Check whether the site collection has retention policy is enabled.
4.Try to increase the site collection quota, then delete files.
5.Try to use PowerShell to delete files.
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