A mix-up is definitely not cheating in Harem/RH Stories. If you wanted it to be completely ironclad (and if your story is already supporting multiple POVs) you could make sure the reader knows in advance that MMC #1 is cool with it, but it's not strictly necessary for the audience to know it's a mixup from the get-go.
The thing about beta readers is even when they're 100% right in a general sense, they can also be wrong if they aren't readers of your niche. in RH/Harem/Poly/Menage this is even more true than usual, as the divide between people who are monogamous heart and soul (one true love) and people who are open to multiple loves is massive. I'm not going to get deep into that now, but if your beta reader isn't writing/reading RH, then she might be transferring certain monogamous ideals onto a story centered around non-monogamy.
Personally, as someone more or less in your niche (well, a close cousin to your niche) it doesn't sound like an issue to me.