Hi there and welcome to the forums 
This is a specific bug with Hyenas that a few of us have encountered - the ones that are going missing are all the ones that would have been Greater Hyenas. Please see the thread below for further info
For what it’s worth - since you’re on singleplayer, you could use a pseudo-workaround - it is very clear from testing that it is each and every greater hyena that is going missing, so you could use the admin panel to spawn the missing ones in as adults - at least that way you don’t have to ‘lose’ any more while waiting for the fix.