The cause of what you're seeing is usually another application that is consuming a high percentage of system resources, particularly CPU, even if it's only momentary.

To keep from adversely affecting other programs on your computer, the game was designed to yield priority to any applications or processes that are running on the computer, even if they are background processes such as Windows system tasks or anti-virus protection processes. If there's a 'spike' in usage, the game may appear to halt momentarily as it yields resources to the application with higher priority.