The PTP protocol cannot work correctly over an LACP bond when the bonded interfaces connect to different Boundary Clocks. This is because each Boundary Clock has a unique clock identifier.
The PTP slave can receive sync/followup messages on one link, but it is non-deterministic which link it will send the delay-request messages on. When delay-request is sent on another link in the bond, delay-response messages returned will be from a different clock to the clock identified in the sync/followup messages and will be ignored by the PTP slave.