Posted by Because it is a solid fat at room temperature. Neem oil is high in stearic and palmitic acids, which set below about 20 °C, while its oleic acid stays liquid a little longer. As the bottle cools, the fats set at different rates, so you get a clear liquid with pale blobs floating in it, a waxy cap on top, or a bottle that has gone solid all the way through. Nothing has grown in it and it has not gone off.
Stand the bottle in a bowl of hot tap water for ten minutes and shake it, and it will be clear and pourable again. A bottle that has frozen in a cold shed is fine once it has warmed through. Do not microwave it.
If the oil smells sour or like old paint rather than nutty and sulphurous, it has oxidised, which happens to old oil or oil kept somewhere warm and bright. Our storage page explains how to avoid that.