This can be due to either:
The comedian performing the material poorly.
An obnoxious, aggressive, or just generally shitty crowd, or rather, that the crowd and the comedian weren't meshing, weren't on the same page comedically.
The expression is used in both cases. The expression seems to be popular with, and may have originated with comedians from the East Coast, particularly Boston; Bill Burr and Jim Norton are examples of comics who frequently use the expression.