If an incoming email has the same (f.e. empty) subject, the emails are incorrect listed. For example, first I write person B and months later person C with the same subject "(no subject)" (but there are completely different emails), then I get an incorrect incoming message tree because both conversations are mixed to 1 conversation and the in the emails included Message-ID respectively References(-ID) get ignored.
Presumably, if I understand you correctly, you need to go to the /Configuration/Preferences/Display/Summaries page, and uncheck 'Thread using subject in addition to standard headers'