Actually, I've never thought much about it even though Japanese is my mother tongue. Now, I can see a credible explanation about it in the link allhailhata gave us and
五十音 - Wikipedia.
Needless to say, I could ask furthermore "Then, how and why in Sanskrit in the first place ?". In the case of Gojūon in Japanese at least, however, those explanations would make sense.
GreyWolf, thank you for your posting. If you had not started this thread, I would have known nothing about it.