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Funny that you mention it, because last week the same problem happened to me... And this was AFTER the magnetic port of my phone got loose due to the use of a third party Magnetic Adapter...
The REAL problem here is a bad design of the phone's covers AND magnetic port, because as a Mechanical Engineer with design experience I would have made the magnetic port unable to extract from outside and at least making it "clip" besides the crappy double-sided-adhesive-tape that was used...
Anyway my phone was bought on New Zealand and I live in Venezuela so I had zero (0) warranties whasoever so my solution will be to go to this place http://www.witrigs.com/accessories-for-sony-xperia-z3-compact and buy both the Covers and the Magnetic Port again (since mine broke after trying to glue it) and this time I will use Hardcore Epoxy.
I will definitely post my results here.
BTW at least the replacements are not that expensive... $8 for both covers and $6 for the magnetic port. I will try my best to make it Waterproof again.
Diego.