What you're talking about is a common mental pattern of attributing bad intent where there is none. Sometimes called "siege mentality". It's a definite problem, and many communication manuals talk about practicing adopting perspectives that avoid it.
You're right about how one's desire to see something a specific way has a huge influence on what they actually think. However, that tends to be counter-productive both ways.
You might choose to ignore the problems because you have to succeed despite them. That's generally how immigrant Chinese people look at the bigotry directed towards them. As a side effect, the Chinese community has issues talking about what that bigotry actually is.
Alternately, you might choose to try to root out the subtle effects that make up the bulk of bigotry, like the feminist movement. So there's a lot of academic language around defining the nature of misogyny, but you get accused of seeing bigotry where there is none because it's heavily contextual.
We want to latch on to egregious moments as catalysts of change, but the real problem is the low level background noise where you have situation after situation where it's unclear how to interpret a specific event. Case in point, I've seen female friends dealing with situations where their mentor probably just hit on them, but it's deniable enough that you can't necessarily call it out. Depending on which glasses you're wearing, you can choose to see it however you want, but the problem is that every female colleague or friend I've talked to can recall instances of ambiguous unwelcome advances mixed into their professional interactions. There's a problem, and it's not just a matter of which glasses they're wearing.