There are many reasons for that to happen. One of the most known is that "the cheapest is not always the best deal". In many cases, the lowest bidder might be known for not delivering good projects. Maybe paying a little more for something more beautiful or safer is the best way to go. Most likely it is.
One of the most legitimate reasons for not going with the lowest bidder, also, is time. If a bidder is a bit more expansive but it can deliver the project is a tighter schedule. In case this is needed or urgente, it might also be the best way to go.