In any case of severer life threatening illness your vet should be your first choice for medical assistance in this case though you have indicated you are feeding timothy hay based dark colored food pellets. These three related questions can assist you in balancing the diet of rabbit as it relates to alfalfa consumption and weaning. 

* http://pets.stackexchange.com/questions/5910
* http://pets.stackexchange.com/questions/1460
* http://pets.stackexchange.com/questions/3108

While the high food value of alfalfa is a concern, it **may** be a requirement for breeding rabbits [(*ref*)](http://www.rabbit.org/journal/3-3/fiber.html) it should be pointed out that there are many different lines of thought here, so discuss nutrition with your vet to make the best choices for your rabbits.  Rabbits are dependent on a high volume low value food supply, but in captivity and in breeding programs there can be issues.  In particular nutritional care for rabbits living in wire bottom cages can be problematic as it can interfere with [cecotrope consumption](http://pets.stackexchange.com/questions/617).

Along with the other critical information you refuse to provide to assist in answering this question, you have neglected to include the breed.  A litter size of 3 is [small for most breeds of rabbits](http://pets.stackexchange.com/questions/5877/how-fast-do-rabbits-really-breed), which can also be an indicator of poor nutrition. Based on the available information and your second question http://pets.stackexchange.com/questions/7417, it is likely that you are failing to meet the nutritional requirements of your rabbits. 

Lastly there are several variables in kit survival rates, not all are well understood. [(ref)](http://riunet.upv.es/bitstream/handle/10251/10222/427-783-1-SM.pdf?...1) [(ref)](http://www.ncbi.nlm.nih.gov/pubmed/9110203) Mortality rates of 10% to 100% can occur, even if you are doing everything correctly, expecting all kits to survive is not realistic.