Hello Noam (and everyone else),

Thanks for your quick response.

The patch you provided does indeed seem to fix the issue, or at least it 
hasn't happened for the time I tested it (I can verify various processes 
were running and outputting things to the async buffer).

I do not have any idea as to why did those markers get swapped around. 
Is there any specific place that deals with them that I could check? 
Could this be a bug with comint mode, maybe clashing with another package?

This is my list of installed packages, directly from package-list-packages:

|  atom-dark-theme    20181022.1602 installed             An Emacs port 
of the Atom Dark theme from Atom.io.
   atom-one-dark-theme 20190705.554  installed             Atom One Dark 
color theme
   avy                20200311.1106 installed             Jump to 
arbitrary positions in visible text and select text quickly.
   cmake-ide          20190731.1009 installed             Calls CMake to 
find out include paths and other compiler flags
   cmake-mode         20190710.1319 installed major-mode for editing 
CMake sources
   company-quickhelp  20180525.1003 installed             Popup 
documentation for completion candidates
   company-rtags      20191222.920  installed             RTags back-end 
for company
   dockerfile-mode    20200106.2126 installed             Major mode for 
editing Docker's Dockerfiles
   elpy               20200326.2207 installed             Emacs Python 
Development Environment
   exwm               0.23          installed             Emacs X Window 
Manager
   glsl-mode          20191017.2148 installed             major mode for 
Open GLSL shader files
   gruvbox-theme      20200307.1522 installed             A retro-groove 
colour theme for Emacs
   helm               20200325.757  installed             Helm is an 
Emacs incremental and narrowing framework
   key-chord          20160227.1238 installed             map pairs of 
simultaneously pressed keys to commands
   powerline          20200105.2053 installed             Rewrite of 
Powerline
   smartparens        20200324.2147 installed             Automatic 
insertion, wrapping and paredit-like navigation with user defined pairs.
   sudo-edit          20180731.1908 installed             Open files as 
another user
   swiper             20200319.1334 installed             Isearch with 
an overview. Oh, man!
   zerodark-theme     20190528.923  installed             A dark, medium 
contrast theme for Emacs
|

If needed I can post (potentially) relevant fragments of my 
configuration files.

Kind regards,

Jacob