A Fibonacci heap is a data structure for priority queue / heap operations. It seems to have the best complexity for all operations:
Since it has the best performance, why not use it everywhere? What are the disadvantages of it?
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$O(1)$ merely means that no matter how large your heap grows, the operation will always take roughly the same time to execute. It doesn't mean "the fastest".
Wikipedia article you linked has section named "Practical considerations":
Fibonacci heaps have a reputation for being slow in practice due to large memory consumption per node and high constant factors on all operations. Recent experimental results suggest that Fibonacci heaps are more efficient in practice than most of its later derivatives, including quake heaps, violation heaps, strict Fibonacci heaps, rank pairing heaps, but less efficient than either pairing heaps or array-based heaps.