We are a small startup company with 2-3 project running simultaneously by 3 developers and 1 QA guy. We use Scrum and we encountered difficulties while we had a sprint with a user story, as small as we could shrink it, with more points than the sprint could hold.

We didn't want to estimate the tasks because we believe a user story is the smallest resolution we should price. Another example situation would involve a smaller volume user story that we didn't finish at the end of the sprint (1 Point = 1 Day).

What is best way to handle these cases in aspects of:  

 1. Counting points for planning and execution of current and next sprint.  
 2. Monitoring progress during and over sprints.