No single product is 100% foolproof and can prevent, detect and remove all threats at any given time. Just because an anti-virus detected threats which Malwarebytes missed, does not make it more effective as both are needed...they scan for different things.
Further, the security community is in a constant state of change as new infections appear and it takes time for them to be reported, samples collected, analyzed, and tested by anti-vendors. Security vendors use different scanning engines and different detection methods such as
heuristic analysis or
behavioral analysis which can account for discrepancies in scanning outcomes. Depending on how often the anti-virus or anti-malware database is updated can also account for differences in threat detections.
When compared to other security tools like Spybot S&D and Ad-Aware, the
advantage of Malwarebytes Anti-Malware is that it uses a
proprietary low level driver similar to some anti-rootkit (ARK) scanners to locate hidden files and
special techniques which enable it to detect a wide spectrum of threats including active rootkits. IMO it has proven more effective than many of the stand-alone ARK tools which are available. Malwarebytes
intentionally does not search for and remove cookies which pose no significant threat. The research team investigates new rogue applications and malicious files so the database is usually updated several times a day in an aggressive effort to keep it current. Scanning is performed quickly while other tools can take hours.
Malwarebytes Anti-Malware is designed to remove malware as effectively with a Quick Scan as it will with a Full Scan which takes much longer to complete. Both scans use
heuristics that bypasses polymorphic blackhat packers & encryption,
MD5 Hash, check memory (loaded .exes and .dlls), unique strings, autostart load points and hotspots (everywhere current malware is known to load from) and multiple other malware checks which are not discussed in public to safeguard the program from malware writers who would use that information for nefarious purposes.
You may also want to read:
Glossary of Malware Related Terms