So I recently have gotten HTTPS errors on Chromium (on trusted sites) returning the following:
I am on Xubuntu Xenial Xerus 16.04 for reference.
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It's an Ubuntu bug with Chrome 53, so simply upgrade to a newer version.
Certificate transparency is a way for Google Chrome (and any other browser that chooses to use it) to verify that a certificate has been issued legitimately - not incorrectly or maliciously.
For a certificate that is marked as transparency enabled (it has an oid of 220.127.116.11.4.1.1118.104.22.168 in the certificate). Chrome will check the certificate transparency logs of the issuing certificate authority to make sure the certificate is present.
However, some certificate authorities choose to redact part of the domain name in the logs - particularly for private resources.
The most likely scenario here is that Namecheap has requested the transparency logs be redacted for files.namecheap.com at Geotrust (the issuer) and so Google Chrome cannot verify the certificate was issued legitimately.
Your option here is to raise a ticket with Namecheap and see if they can issue a cert without redaction, and in the meantime add an exception (if you are willing to trust the certificate).