Ever since I finished heljarchen hall(nearly) I haven't been able to find glass, straw or goat horns in stores on top of that I haven't been able to find goats either. Is this a bug or just comically horrible luck and if it is a bug is there any way to fix it?

I have noticed this too and am unsure of the cause. It is a known bug according the http://www.uesp.net/wiki/Skyrim:Hearthfire#Bugs. There seems to be no known fix for it like many other bugs in the game.

Goat horns, straw, and glass are available from general merchants (in cities) and Khajiit caravans and under normal circumstances were supposed to reset (restock) every 48 hours from these merchants. Additionally, I have noticed that straw and glass can be found in much smaller quantities as random loot in containers (such as cupboards) in dungeons, homes, and certain other interior locations. As you probably are aware, goat horns can be obtained from killing goats out in the wilderness (although not all have horns when looted). Goats and other animals in wilderness areas are supposed to respawn every 10 days, but you will have to not visit such areas for 10 or more days or else the respawn timer will reset. If these methods fail, you can always have your steward furnish your home (assuming you've hired one), although this understandably may take the fun out of building the house yourself.

There is also a known bug where sometimes animals do not ever respawn for unknown reasons, although I have never experienced this with problem with goats personally.