It seems that it is not a common issue per my test. However, we can work together to narrow down and resolve the situation. So, please kindly provide more information below to let us work further.
1.Which method did you use to delete the file? UI? Or some codes?
2.Whether one file or some files occur this issue? If there are some files occur this issue, are they in the same folder?
3.Please check whether the file has unique permission?
4.Make sure the file is checked in, published and approved.
5.Make sure the file is not opened by multiple people at the same time.
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