It depends on the complaint. You can force SA to align on very few stars.
Often the issue is hot pixels... especially when OSC or CMOS is implicated with very short exposures.
(I would bet some good money your exposures are very short if you have 100 of them!)
The other thing is the out-of-focus stars can be problematic.
How about more information like the camera used and a full scale jpeg showing the stars in your data?
Finally, it should be said that you need SA initially to produce star-aligned images. But then. CometAlignment process will actually align the comet without the need of stars (you will click on the comet).
-adam