The phrase "Let it happen" can often be used in a situation where someone may be trying to force something e.g. relationships, conversations, sexual encounters, sports, image, ect. This phrase is mainly used for advice for friends, but may not always be the right thing to do. The phrase is often used incorrectly in awkward situations, this is wrong. Usage of this phrase has to feel right, do not force usage as you would be contradicting as well as disgracing its meaning. This phrase accompanies a sort of ideology that some things are meant to happen, others are not, therefore one should not force things.
Guy: "Man I really want things to work out with Susie, but I'm not sure if I should force it or not"
Friend:"Dude, let it happen."