Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

     https://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org mailing list.
------------------------------------------------------------------------
This is a simplified reproducer of the problem, as discovered by user
@lyndhurst on SE Emacs. See
https://emacs.stackexchange.com/questions/82261/set-org-babel-source-block-parameters-dynamically
for more details.

Starting with `emacs -Q', open the following file:

--8<---------------cut here---------------start------------->8---
* Bug report example

#+begin_src shell
  echo "foo"
#+end_src

* Code

#+begin_src elisp :results raw
  (setq org-babel-default-header-args:shell '((:results . "file") (:file . "results.txt") (:output-dir . "a")))
#+end_src
--8<---------------cut here---------------end--------------->8---

Evaluate the last code block to set
`org-babel-default-header-args:shell' to the indicated value, then
evaluate the shell code block repeatedly: the first time it works to
produce an output file `a/results.txt'; subsequent evaluations produce
errors:

org-ctrl-c-ctrl-c: Opening output file: No such file or directory, .../a/a/results.txt
org-ctrl-c-ctrl-c: Opening output file: No such file or directory, .../a/a/a/results.txt
org-ctrl-c-ctrl-c: Opening output file: No such file or directory, .../a/a/a/a/results.txt

Note the increasing number of copies of the `output-dir' setting.  
The value of `org-babel-default-header-args:shell' is modified every
time:

    ((:results . "file") (:file . "a/a/a/a/results.txt") (:output-dir . "a"))

The problem is the way that `org-babel-get-src-block-info' constructs
the `info' variable, which is used to pass around information during the
evaluation: the value depends on the `org-babel-default-header-args*'
variables, but is modified in place, and because of shared list
structure, the modification gets propagated to the user variables.

Emacs  : GNU Emacs 31.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.43, cairo version 1.18.0) of 2024-08-09
Package: Org mode version 9.8-pre (release_9.7.10-127-g07dd3b @/usr/local/share/emacs/site-lisp/org/)

------------------------------------------------------------------
The following patch wraps calls to `copy-tree' around the relevant
places to eliminate the sharing.