Theory busted....
I reset all formation subs to 50.
I make 44 subs, all in 3-4 formations.
I changed my coach philosophy to use a 4-3 PB instead (which of course has no 3-4 formations).
I then reset my subs. By my theory, since the game couldn't find any of the formations that had subs in it, it wouldn't be able to reset them so I'd only have 6 (50-44) subs available.
I was still able to make all 50 subs in my 4-3 formations.
EDIT:
I have no clue why the game behaves differently for you.