We have been seeing a similar issue of a hop during landing in altitude and position control modes. The aircraft will touch down then throttle up and maintain a centimeter high hover even with full stick down. We've flipped a couple aircraft when a leg touches and breeze hits during this several second ordeal.
We've partially solved the issue by changing EKF2_HGT_MODE to GPS (1) from Baro (0). Our conclusion is that the prop wash is causing an estimated altitude drop and the mc_pos_control is fighting that and taking it into a hover.
We're are looking at improving our enclosure around the Cube to prevent external wind and prop wash from affecting the internal baro measurement.''
Here is an example plot. The landing occurs around 13 seconds and from there until the actual landing detected the operator had the throttle stick fully down.