So, you get into the planche position, with kees touching your elbows, and whilst holding that position, your knees 'crack' like if you crunched your knuckles?
If that's right, then it is more than likely just the kneecaps moving slightly, or release of pressure in the joint capsule caused by the extreme contraction of the hamstrings in that position - your legs are at max. flexion, then you are tensing the leg muscles staticaly as you hold the position, so the knee is as bent as it can get. Its the exact same situation when you crack your knuckles- they have to be pushed past their natural ROM to get the 'click'. With knuckles, you apply external pressure (pushing em down with your other hand), here you apply it with extra hard pull of the hamstrings.
If it doesnt cause soreness, I wouldnt worry, but if you want to stop it, just try and relax your hamstrings a bit as you find your balance point in the planche.