I have made it to the top of a mountain where a dragon was guarding a wall with a new shout on it. I killed the dragon and I can't seem to absorb the soul. I have definitely never killed him before and I dont appear to have any armor it spell effects that claim to alter anything related to the dragon souls. Is there a way to fix this so I can obtain the soul from the dead dragon?
There could be a few different things going on here. Some which are related to a glitch and other which are not. To cover the no glitches there are 2 things that I can think of. First there is a limit to the amount of souls you can have at any one time. Spend the souls when you can rather than saving them up. The second is that you can only obtain A dragon soul once. If you kill the same dragon a second time, you don't get a soul (yes they come back to life). This was put into the game to stop people from abusing the system while still providing regular dragon encounters.
The second point above is actually the cause of a glitch. Sometimes the game will think that you have killed a dragon before when you might never have done so. If this is the first time you have killed this dragon, which it likely is due to it being at a shout wall, which can also glitch.
The issue was meant to have been fixed in a patch released for the game, so if it is still occurring, check you have the latest patch installed.