I see the only probably reason for such behavior. Your users sent emails using reply-to action to actually send different email to a different receipient. Please open two different emails from this mail thread and review Headers section. If you'll find two identical identifiers then it means that you have to teach users how to use email client.
There may be a lot of references in the email.
subject: Re: Premium support
in_reply_to: CAEvXH2P5n1vgvezSJ_5YCm-QR=-MC1TFsUefOm7EzTQTc_qE2w@mail.example.com
date: Tue, 02 Aug 2016 13:28:45 +0200
messageID: <093fb8128f893aa9475c4cd965ce9126@example.com>
ctype: multipart/alternative
internaldate: 02-Aug-2016 11:28:46 +0000
references: <466624df40679a142cb9a4923b00e736@example.com> <D37638BF.60D26%user@example.com> <ae1b2511aad86469b825b41fd2ee8748@example.com> <D3793941.60DBC%user@example.com> <47655b80a5b860070fcc91c8d0442b76@example.com> <D385FB22.61352%user@example.com> <cd731fc4c247cc6c472fc9d4cf26dbd9@example.com> <D38C87FC.6162D%user@example.com> <16485e818c61e09611558f65919241d9@example.com> <D38DA724.61680%user@example.com> <cb353f10559983011dff0facd3431944@example.com> <D38DB94D.61695%user@example.com> <61a6b0600627c199398f8fba866b789b@example.com> <D39BABE3.61C04%user@example.com> <4ea219c8492d623e366912109901bf08@example.com> <D39CC496.61C34%user@example.com> <5185f751b89a32e93d281046be71091c@example.com> <1F693A28-CB8A-4D59-94E0-515998070682@example.com> <4a38493e436f0ef2241dbe10ea923a03@example.com> <4B4DC6E9-716C-4D95-8F63-6122DF5C0C2B@example.com> <CAEvXH2OaNWn2gm2GZGXtbLEOueCosh1io75Boq_ibAN+aFtYXw@mail.example.com> <D3B46ABA.62216%user@example.com> <7f250cf521630dbcd6e4778a706243a8@example.com> <77a67ebf39db8a3d59d563871005c914@example.com> <4a022fcd16e802b0b3d68606b5103750@example.com> <5D213626-AAF1-4CBB-B99F-A56C5E714A63@example.com> <002eb97646f936f9919ce4823c796abe@example.com> <45E20CFC-C293-4792-A77C-80648111C7DD@example.com> <a338faec548a0816210b86b14b2c4c2f@example.com> <CAEvXH2MUHMvznEyykDzrGdj-aTnxaNcr9qiteJpO_h9KfDC-XQ@mail.example.com> <CAEvXH2NFqYz=xnBngoJzp8cpwZxeb1R_z1-V4aFe00-j=Y8uqw@mail.example.com> <632cf06c56bb8f8206b3c291d2b70b7d@example.com> <CAEvXH2P5n1vgvezSJ_5YCm-QR=-MC1TFsUefOm7EzTQTc_qE2w@mail.example.com>
folder: INBOX