She is probably calling for her friend. How old are they and how long have you had them for? I had this when my piggies were younger and they weren't used to the routine. I would take Velvet out of the hutch and put her in the run and she would immediately start calling for Betsy and when I put Betsy in the run the wheeking stopped. Similarly, as soon as I took Velvet out of the hutch, Betsy would immediately start calling for her. This stopped after a while as they knew that they would meet up again soon.