Plenty of legit things get flagged by anti-virus programs as bad all the time. I've not used Malwarebytes myself so can't say if the same is true for that, but as someone who used to do tech support for another website I can say it's a common enough occurrence with AV programs in general flagging things and blocking them that should not be blocked.

Of course, there's clearly something wrong or you would not have been breached, so better safe than sorry.