Dirty llama has no option to clean. :(

@elvici I have two sheds (one llama and one cow) on a veterinary lot where I have a big family living. I never had that issue there. However, it could be related, since living on a vet lot is a type of 'workaround', as is adding farm animals, I have assumed.

I did have an issue on another lot in which I had MOO/alt-placed a shed for a llama and had a gate opening to the left of the shed (left when facing the front of it) and I think I was maybe one tile short of the green allotted area for the shed. I found there was an action I could not get to pull up at one point (maybe clicking on him to pet/feed/clean?) when he was in that area of the fenced area, he got glitchy (don't fully remember in what ways). I have a friend who had downloaded the lot (I made it) and he never had that issue. I re-situated the area and re-uploaded the lot to the gallery to address it, though, and I never had the issue reoccur. The changes I made was to make sure the allotted area for the shed was fully within the fenced area, that I placed it with MOO off and where it snapped to with no alt-adjustments, and that there was also no overlap with the allotted area for the gate to open or with the chicken coop. 

Does your sim have a good relationship with the llama? Can another household sim clean the llama/get the option? Were you able to clean it previously? Is your sim living on the lot/there every day to clean the llama & shed and feed it?

Can you share a screenshot (top-down) of your shed area (in build mode, with the grid on, and with the shed highlighted)? Also, if you would like to share your lot to the gallery I would be happy to test it in my game: 

Another possibility is that the llama itself is just bugging out for some random reason that has no foundation. If that were the case and resetting the shed and llama is not helping, you could delete the shed, save and leave the lot, then re-enter the lot and add a new shed and buy a new llama for it.