There are a few reasons why a rabbit might leave normally formed cecotrope clusters uneaten. Young or baby rabbits might do it because they are easily distracted by things and may forget to eat them. As they mature they should grow out of this. Older rabbits might leave them uneaten if they are in a new home or area and feeling distracted, or if they are frequently stressed about something such as living in an environment with frequent noises that startle the rabbit, a predator the scares it, etc. Another reason for leaving them uneaten is if the rabbit is obese and has difficulty reaching down there to eat them, or if the rabbit has a medical problem such as spinal issues or arthritis that can make it uncomfortable for them to bend down to eat the cecals.
The most common reason for a healthy adult rabbit that is not obese, to leave uneaten fully formed cecals, is due to a diet that is too rich. The fact that your rabbit is getting alfalfa hay and unlimited pellets could very well explain the uneaten cecals. Even though she is still nursing her litter, you might want to try cutting back some on the alfalfa hay and see if that corrects the problem. Now that the kits are getting older and starting to eat solid food, she may not be needing the extra protein and calcium from the alfalfa, and she will still be be getting plenty of nutrients from her unlimited pellets. That's what I would try anyways, less rich food and more grass hay will usually correct the issue.
If the cecals are not normally formed in blackberry looking clusters, but are coming out improperly formed where they are mushy or pasty, then that is most often due to too many carbs in the diet, either from treats or pellets. Usually the solution is to reduce pellets and feed more grass hay, but with her still nursing and needing the extra pellets for nursing, that would complicate fixing the problem, that is if this is what is going on instead of the clusters being fully formed and normal.