Mail is combining random incoming emails into single jumbled messages
Since upgrading to El Capitan Mail (and some other iCloud-using apps) has nose-dived in reliability. Once or twice a day Mail seems to have a period of merging distinct emails into single emails. Here's an example of a marketing email from Thread (fashion) which has been merged with a marketing email from Planet X (bikes), but there are many more.
I can see individual emails correctly on my iOS and webmail browsers, so the issue is with the desktop Mail app. As well as merging random emails it also, from time to time, pulls emails back in, resetting their 'unread' status and assigning new timestamps to them. It all sounds like an issue with how it communicates with the server.
In case it is relevant, I will also say that iCal and Pages have also crashed and thrown up errors since the El Cap upgrade, having previously been rock steady.
MacBook Pro (Retina, 15-inch, Late 2013), OS X El Capitan (10.11.3)