Me too!!! How bizarre.
7 year old pony has been doing this on and off on different feet when I pick out. I'm very careful, pick up his foot and it's literally as I tilt it upwards slightly before pick it out it feels stiff, then makes this horrible loud single crack noise and it moves freely.
With a young pony and it happening on different corners I thought it must just be like our own joints cracking. Only happened intermittently in the last few weeks and had him almost a year. Very weird
He's certainly not lame though and other than making me cringe is not bothered when it happens to him. You could ring your vet to ask but I'm thinking it is normal.