I'm not sure if I can explain this clearly, but I once encountered a similar issue. It seemed like, when placing reservoirs in the system, they had to be positioned on a streamline only. I had previously tried placing one on a channel, and it seemed to cause problems. So, I solved it by creating a new stream with a smaller threshold area, which allowed the streamlines to be drawn in more detail—and that made it possible to place the reservoir successfully.
Another possible issue is that you might have placed the reservoir overlapping with a lake. It seems the system is designed to support either letting you define a reservoir manually or using the "Add Lake" function—but not both at the same time. (In SWAT, a reservoir is considered a type of lake.)