Hey there!
Sadly, there are times that this does happen.
Is the mother a first time mother? Is she having to raise the babies alone?
These two factors put a lot of stress on a female gerbil.
Usually the male is there to help her with raising the litter, but many times, our house holds aren't big enough as the outdoors and, in being responsible, simply cannot let our animals breed willy nilly. If she's a first time mother, she may not have the benefit of a daughter with her from a last litter that would help her as well.
If the answer to the above is No, then its possible you have an irresponsible mother and I would not breed her again.
It's uncommon for a surrogate mother who is already nursing to reject other pups given to her, but you stated she has 2 1/2 week old pups and this could be the issue.
2 1/2 pups are close to opening their eyes (if they haven't already) and are almost 3 weeks old where they start to begin weaning.
That is too late to try to introduce newborns to surrogate mother with a litter that old. Usually this has to be done when both litters are as close in age as possible and usually a week old or less.
Sadly, in my breeding experience, if the mother is rejecting them or simply will not care for them -- it is practically impossible for us to hand care for pups under 2 weeks of age.
Even at two weeks old, it is still challenging, but can be done. It requires needless syringes and kitten milk, or bread soaked in condensed milk and a couple other intensive methods.
Sometimes the mother rejects pups after they've opened their eyes, I've has this happen, but least by then, they grasp the concept of "the syringe means FOOD" pretty quickly.
Usually in these cases, where I've a newborn litter and the mother isn't caring for them, I pretty much leave the litter with her as I know there is nothing I can do.
Either she will start to care for them, or she won't. And if she won't, sadly they will pass away within a few days of not being fed and then I just dispose of them.
Its hard. I know, trust me, and I am sorry for your painful experience.
If the female is a first time mother, if you are wanting to breed, I usually try her ONE more time. Many times, they are so much better with the 2nd litter.
But if she rejects the second litter, then that female is marked down as unfit for breeding and I go with a new pair.
Sorry this couldn't be more helpful.