Ok, that makes sense, then. Probably there are other users who indeed will rely on clocking in non-agenda files.
The thing which made it hard for me to identify the initial problem was that the test CLOCK lines I had in the testing file where placed there without a heading. When later in the day I wanted to clock in to my tasks, I then just ended up with a "outline-back-to-heading: before first heading" error, but with no indicator which of my ~60 open org files was the culprit. Maybe one could insert the file location in that error message?
Since org is so extremely useful, and I almost spend 80% of my day in org files (also some of my collaborators are beginning to use it... it is viral), I often have >50 files with all kinds of purposes open: agenda, various notes, beamer, html-exports, wiki-authoring, project-organization, bookkeeping... the thing is just too useful. So, I think clashes between the many uses of org files probably are natural.
This being emacs :-) I just decided to advise org-resolve-clocks.
(defun dfeich/org-resolve-clocks (orig-function &optional only-dangling-p prompt-fn last-valid)
(cl-letf (((symbol-function 'org-files-list) 'org-agenda-files))
(apply orig-function only-dangling-p prompt-fn last-valid)))
(advice-add #'org-resolve-clocks :around #'dfeich/org-resolve-clocks)
Thanks for maintaining and developing an environment which made my time in front of the keyboard so much more efficient.