In recent org, org-highlight-links including 'bracket' will hide contentwith double brackets inside src blocks.
A vanilla config loading 9.5.5 org (I did this through straight.el) can reproduce this with a
minimal org file including just:
#+begin_src python
[[a]]
#+end_src
The brackets will be hidden.
I can only confirm that this does not happen with org 9.5.2 - I did not
check other versions in between, but know this has been the case for a
couple of weeks at least. I don't know much of the internals, but
thought that perhaps the issue was introduced around this commit (as this touches link folding and is not included in 9.5.2):
Cheers,
Tim