Online help and manual for "Circulation and Fines Rules" say: "If you are a single library system choose your branch name before creating rules (sometimes having only rules for the 'all libraries' option can cause issues with holds)" Such issues should be considered as bug and need investigation.
First occurence in: Bug 5940 - Update Help Files for 3.4 https://bugs.koha-community.org/bugzilla3/attachment.cgi?id=3545&action=diff
What is wrong? Maybe it is just the manual?
I think it _was_ the manual. I've removed this note since as we have been using the standard rules without issues in a lot of installations and as Marc pointed out, we should not have notes like this in the manual, but fix any bugs that might occur.