Heh, yeah that didn't actually make it into the fluff, the current reason is that Commander Farsight and the other Tau warriors behaved with utmost honour in recognising the function of Apothecaries, and allowing them to go about their business of harvesting the gene-seed of the fallen unmolested, that they earned the 'warrior-respect' of the Astartes.
What book is this from?
The Farsight supplement.
It's funny though incorrect.... because Tau and the Kroot come from different planets and during the great crusades they hadn't met each other. But beyond this slight detail it's indeed very funny. ^^
There is also the other reason that is in the old codex: space marines; tau and ultra-* were battling on a relic planet, then necrons awoke (awesome luck) and started attacking both armies. Marneus decided to make a "tactical fall back" (flee form the scene) followed by "mass xeno cleasing operation". However, since the tau warriors started shotting only at the necrons, he somehow, decided to warn then of the bombing, and ordered his troops to ignore the tau while shotting only to the necrons. He also allowed the tau to leave the planet airspace before sending the "inquisitorial regards" (exterminatus) to the necrons (even if they didn't have inquisitors with them at the time)
Suuuure let's just ignore that Space Marines are supposed to be unstoppable demigods as the fluff builds.
They are unstoppable only occasionally after all there are chapters that have been wiped out, suffered major defeats and losses. hell that is part of the setting, no one side can nor should be undefeated nor invinsible... though marines come close, but it's nothing destroyers or shit ton of tesla fire wont fix :D.
or if you ment just the primarchs, sure they were only defeated by hands of their brothers but that is what makes this one so funny.
Dark Space Elves
Titans & Knights
Ye Olde WMS