Your website probably has too many files, when the Sucuri scanner tries to inspect them all searching for malware, your server stops the operation after the maximum execution time (which is a value set by your hosting provider) is reached.
Talk with your hosting provider to either increase the value for this setting, or to go the plugin settings’ page and select directories that you don’t want to scan, that way the scanner will take less time to run and the server will not kill the script.
Let me know if you need more information.
