'Is it OK to use both McAfee and Malware?'
I'll assume you meant using McAfee and MalwareBYTEs together and YES, you can use them both together.. Just an explanation about the tech's information.. First, there HAS been a couple of false positives recently for which Malwarebytes identified ONE of McAfee's files as malware.. Upon removal by Malwarebytes, McAfee would no longer run.. I believe that has been fixed at this time. As with all tools, be watchful and careful which files those tools are removing.
In addition, depending on which version of McAfee you have running, the McAfee suites now include an antispyware tool which could conflict with another antispyware program IF both are running "real time" in the background.. The free version of Malwarebytes does NOT run realtime in the background so that's not really any issue for most unless you're using the "paid-for" version. Also, in my opinion, we're seeing way too many spyware infections from those using the McAfee antispyware tool. It's just not doing an effective job. On the McAfee forums, our cleanup advise is to use other removal tools such as Malwarebytes or SuperAntispyware. They find and remove malware that McAfee isn't.
Simply stated, although it's possible the program "may" have removed one or two files incorrectly, the reason your computer ran better after using Malwarebytes is because it cleaned out infected files that McAfee did not..
Hope this helps.
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