A lot of athletes have their heels kick their butt while running.
How do you get rid of it? Any good exercises?
Is this a bad thing?
I would be thinking that if the heel can get closer to the butt at some point through the recovery phase, it is able to take a bigger bite of the ground. Not to mention the efficiency in preparation in lifting the knee before the foot goes toward ground again.
Thoughts?
your heel is NEVER supposed to kick your butt. it is supposed to hit your hamstring.
I mean before the knee pass the other one and when the knee points down, the heel should not be much higher then the knee - in fact, the heel should never go higher then the knee.
Reason is when the heel hits the butt before the knee has passed the other knee, the heel will bounce back/down resulting in poor knee lift - like in the end of a race.
Improved posture will limit that from happening, to some degree.
check for position of the pelvis. It shouldn’t be tilted at all; it should be neutral. If it’s in the right position when running, that should eliminate your excessively high back-kick - and probably 20 other issues. 
I video clip would really help.
Developing strength and working on technique using tempo/drills will fix thise.
As Pioneer and KK rightly said, think about your posture during drills and running. When doing drills work on keeping the heel under the butt as opposed to behind it.
skip for height
stairs (one step)
strengthen lower abs
pelvic tilts
“step over drive down” cue