Taking control of craft from tracking station killing off horizontal velocity and instead replacing it with vertical velocity towards kerbin

[ConvairNexus]

I was warping to a transfer window from a craft on the ground to be able to timewarp faster and once I got my desired transfer window I went to the tracking station and went to take control of my craft in LKO, once I loaded it in the craft did a jolt and it started falling towards kerbin though it kept its original orbital velocity, When I checked the map it was going into a straight line towards kerbin.