My phone was physically accessed?

Friends, i am sorry if there are plenty of questions like this one but please help me with this one. Me and my sister had to share an apartment with a guy with some mental issues (dont ask why), the guy also happens to be good with hacks and all kind of stuff. We left already but he keeps harassing my sister, he told her that he hacked both of our phones and know everything we do? She is freaked out but i think he is just trying to make us loose. Mine was always protected with password but hers wasn't. Now i had Reset to factory settings both phones and than downloaded malwarebytes and scanned with it but nothing showed up. A friend of ours told us to check if our phones were rooted with Root Checker program, downloadable from Google store, we bouth checked and according to the app we dont have Root permission. Can he somehow rooted the devices, installed something and unrooted it again, also can ir survive factory reset and scan with malwarebytes? The guy may had physical access while we were asleep :s s

Thanks all for your support!

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