For some reason my game has glitched and I cannot take large antlers from elk or deer. I really want to mount some heads on my walls so this is very annoying. Anyone know of a way to fix this?

Well, you can always check the alchemy shops.

the deers shed there antlers when they heard that now the dragonborn will be hunting them for trophys

Just thought the same thing as OP when an Elk walked right up to me and I obviously killed it because I wanted the antlers for the mounted head. No antlers. Not 2 minutes later wandering the woods and roads around Lakeview Manor, another Elk walked right up to me, so I killed it, and it had large antlers. Just gotta keep "hunting, I guess..." total fluke.
On a side note, the manniquin in the upstairs Lakeview main hall was standing about a foot in front of the base on the stand and had nothing equipped (although he was actually wearing around 8 items when I accessed it on the menu screen) weird stuff man. Arvak's floating skull was pretty trippy too.

Luck of the draw. Worse case scenario, buy upgrades from steward.

You can go for ages and not get antlers off them, try a different location.

I spent a long time killing elk looking for large antlers. Even the elk that had large antlers visually on them did not have any antlers to take from them once I tried to loot them. But eventually I did come across the odd elk that did give me large antlers. I don't think its a bug that you don't always get large antlers. They are just rare to find making the whole hunting process a but more challenging.

Just like WoW quests.. you are told to go collect eyeballs and yet every quest target doesn't seem to have them even though they should

Having two characters who like to collect alchemy ingredients, I can tell you large antlers are rare, and small antlers are even harder to get. Pretty sure we need 1 set of small antlers somewhere. And no the stores do not usually sell them so you are going to have to go killing every elk in Skyrim. I would start with the two inquisitive elk who usually hang around the house sites. I would suspect they would have a higher rate of antlers than usual elk.

I have not actually had to go hunting for antlers, since both my characters already had a good supply, the second character is running out of sabre cat teeth though, and unless she gets the steward to furnish most of one house, she is going to shortly be hunting goats with a vengeance. It is no wonder it takes the stewards so long to furnish if they have to hunt for all those antlers and goat horns.

I'm having a problem with the sabre cats giving me their teeth, and none of the stores seem to sell them.

Are you hunting snowy sabre cats? if not go to a colder area. You will need more of their pelts anyway.