Miscommunication isn't the end of the world, no. But women are still being told that they should be careful, and not lead men on, and if men get the wrong impression then it's All The Woman's Fault And She Had It Coming. Accidental flirting can lead to dangerous situations, and at the very least it can make either party feel very uncomfortable.
To expand on the "very uncomfortable" part, hitting on someone is much more intrusive, potentially, than a random conversation. A lot of women are "flirted" with a lot, often to the point of harassment, and are not likely to exactly jump for joy when someone initiates an interaction that reads as an attempt at flirting.
Men, in my experience, seem to be oblivious to how tiresome and stressful this is to many women, even when the men in question are not themselves creeps or anything. They tend to have no idea of the sheer volume of unwanted advances women receive, and are sceptical even when told straight up it can be an issue.
EDIT: also, hitting on someone, unlike random spontaneous friendliness, tends to come with unstated goals or expectations attached. Which in itself is intimidating, because a subset of men large enough to be a problem feel entitled to, and react negatively to not getting, what they want (even if "what they want" is just something theoretically innocuous like attention).