Be-trees were invented in 2003, predating the Tokutek patent: see citation [1] in http://supertech.csail.mit.edu/papers/BenderFaJa15.pdf . I think Tokutek was originally not aware of Be-trees and only later discovered the similarity to Be-trees.
"(...) The Bε-tree has since been used by both the high-performance, commercial TokuDB database [4] and the BetrFS research file system [5]. (...)"
First citation from the paper links to http://perso.ens-lyon.fr/loris.marchal/docs-data-aware/broda... – is this the paper you're referring to as prior-art for Bε-trees?
My understanding is that Be-trees are not covered by a valid patent, either because of clear prior art or because Tokutek patented a different data structure. Be-trees are simpler than the original fractal tree afaik (they were not aware of Be-trees at the time of their innovation).