lsattr shows extended file attributes on Linux filesystems. These attributes are separate from normal permissions and can explain why a file behaves differently than expected.
List attributes for a file
lsattr filename
List attributes in a directory
lsattr
Check attributes recursively
lsattr -R /path/to/directory
One important attribute is i, which means immutable. A file with the immutable attribute cannot be modified or deleted until that attribute is removed.
To change attributes, use chattr. To only inspect them, use lsattr.