I'm grinning because I've mostly had the identical situation only roles reversed.
My mate is just one of those big hearted, naive, trusting people who wants to love the world and believe the best about everyone until proven different.
And because I believe in this high (but stupid) ideal, I have often let things get started even if my warning bells were going off. But over time our communication has gotten better and she's learned to respect my bells - much as I do hers.
This is key because in many situations we've seen, the person who's bells are ringing is accused of being controlling ! It takes some time for people to develop enough trust in each other's judgement and analysis to put this (control) thing away and step back and take an honest look/listen.
Like you, we've discovered that we are seldom if ever wrong about our instincts. Maybe we've lived long enough and practiced enough to hone our skills of observation. Or maybe we're just lucky
I say - keep raising the alarm when you feel it's legit - but make sure there's some facts behind it whenever possible.