At the end of Prometheus, E. Shaw helps David to help her on the mission to ask the Engineers why humans were created. David was in a pretty bad state and needed Shaw's help. Basically becoming indebted to Shaw.
So why, in Alien: Covenant, does David wipe out the Engineer planet with the alien virus?
I presume it's for testing purposes, but wouldn't have Shaw stopped him? David states in the film that Shaw showed the most compassion towards him and that he loved her. So why would he go against her intentions with the Engineers?
Adding to this, if she was dead long before the bombardment, wouldn't David have kept her dying wish of asking the questions instead of bombing them?