Hello and thanks for researching this very important question!
I doubt very much that careful handling is to blame for this unfortunate turn of events...rough play or squeezing can potentially harm unborn young.
Guinea pigs, like people, can miscarry for a variety of reasons, including: stress, poor nutrition, developmental defects in the babies, viral infections, and hormonal problems.
The bleeding does concern me...you might want to have this little one examined by a veterinarian who is familiar with GP medicine to make sure that she is not in an emergency condition at this time:
Please make sure to offer he a diet rich in vitamins C and K at this time, to help get her back on her feet...the best quality vitamin C supplements can be found at the regular pharmacy (pediatric liquid--20mg daily for 2 weeks, then 10mg daily thereafter). Vitamin K is found in dark greens, like kale and spinach--small amounts daily. Her regular food pellets should be labelled for GPs (not rabbits), and fresh Alfalfa Hay can be offered to increase her protein intake.
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