Duplicate owner certificates

[pixelpadre]

Duplicate certificates are creating non trusted 2nd certificate.  Upon checking ssllabs.com I noticed that all of my domains on 2 different servers are getting a red flag due to duplicate owners as explained to me by letsencrypt forum.  Why do we have .bundle and .cert if one has the same info as the other?  I tried deleting .cert and apache would not restart.

whats the deal?