There were numerous bug fixes in Vanilla that did not make it into Classic WoW that had to be patched in after the fact that according to the “reference client” would have allowed these bugs to persist in Classic WoW.
Its fairly obvious that the reference client is not exactly a pure duplicate of Vanilla 1.12, even though they may have rebuilt the 1.12 client, this does not mean that the complete set of hotfixes and patches to bugs in Vanilla were included in build.
As a result the reference client shows a certain behavior, but that behavior did not match vanilla, and thus we have:
Because if the reference client was perfect then we would not have this massive long list of things that blizzard fixed.