I'm having the same issues. Mail body that was previously downloaded sometimes is not shown (only a blank space underneath the message header info).
Sometimes if a message doesn't show, I can go to another message and then back to the one that didn't show, and it will show correctly, or by double clicking the message and opening it in a new window.
I'm running El Capitan 10.11.1 and Mail 9.1 (3096.5). 2 mail accounts, both are Gmail and set up to use IMAP.
I suspect it is an application performance issue, since restarting the application seems to solve the problem temporarily (clearing memory/cache?), and thereafter the problems start occurring more and more frequently through the day eventually becoming almost unusable. Might be related to the fact that gmail accounts usually have very large mailboxes (i.e: all mail) and aren't used to deleting mails (such is my case) and sometimes have several labels/folders which seem to complicate the local mailbox size and structure.