See here : http://manual.koha-community.org/3.8/en/stafflists.html#mergebibrecs the merging bib records tool used to stop you from adding fields if they were not repeatable, but I was just able to add the two 001 fields to my destination record but the framework says it's not repeatable. For the 999 it didn't add it but didn't give me an error either.
I did not test, but I think bug 8064 fixes this issue.
I believe this is fixed. When checking the checkbox to get the second 001 or 245$a: The field is non-repeatable and already exists in the destination record. Therefore, you cannot add it.
*** Bug 10551 has been marked as a duplicate of this bug. ***