Vegapunk tried to replicate Kaido’s fruit and “FAILED”, that’s at least what the World Government and CP0 knew.
Then Admiral Green Bull came to Wano and he saw ANOTHER dragon with the same abilities as Kaido.
I believe that Aramaki, once he returned to Mary Geoise, warned the Marines that Vegapunk lied about the fruit and now the World Government no longer trusts him.
The World Government wants to kill Vegapunk since he’s become more of a threat than an asset. He has fulfilled his purpose, and the World Government doesn’t need him now with the new Seraphims.
As Lucci suggested the reason because they want to kill Vegapunk might be connected to Lulusia.
Vegapunk might be somehow connected to the weapon that Im used to destroy Lulusia (many had speculated it could be the ancient weapon Uranus but it could also be a weapon created by Vegapunk). However, why kill “the most useful person in the world”? Well Vegapunk secretly might have been creating things that are capable of bringing down the World Government. Furthermore he probably have discovered every single secret of the Void Century or might have solved the mystery of Laugh Tale.