This is a humorous exageration. However, it may be true that payroll data can be corrupted or improperly accessed due to software and systems by independent providers, as they may themselves become victims to hackers or system errors. The vender's naive honestly and Dilbert's realization that his clueless manager was right is especially funny.
This still would have worked if Mr. Vendor looked like he was being sarcastic as he spoke. (Maybe even funnier that way? Dilbert would be thinking "Shoot Me" out of massive embarrassment.) But the wide-eyed, no-eyebrows expression (in Scott Adam's world) means Mr. V. is innocently telling the truth and didn't even consider lying about his psychotically-designed product. His company must be another one much like Dilbert's. (But then, aren't *all* big companies like Dilbert's?)