I Dont Understand

No Dumb questions on here. Maybe just some dumb answers at times though
PCGS etc. put there own values on their slabs.
Usually a little higher than the actual price obtained
but not always. Checking ebays completed listings will give you an average of what a certain coin sold for so a decent ball park anyway. That is at least on a genuine coin.
Heritage, Stacks Bowers etc. could get prices at all kinds of different levels. Your comparisons seem to be way off kilter though. Wondering why myself. If the ones that you saw on Heritage are actually completed auctions then I guess it is just one of those, one mans treasure is another mans junk so to speak. Or whatever the buyer is willing to pay is just that.

I am not sure what the circumstances are between the coins you are talking about but I am guessing it is different grades selling for different prices. If there is only 5 coins graded MS-68 they will sell for allot more than it would if there was 900 in MS-68. Its usually condition census that causes the value to jump if its not a key date and even then condition will add allot of value also

You are not looking at values for the "exact same coin", you are looking at values for coins in different grades. Those 1960s Kennedys are quite common through MS65 grades but they take a sizable leap in value at MS66 and they are truly rare and valuable in MS67.

Here is an example: all are 1972p non DDO's All are ms65 and prices go from $7-56?
http://www.pcgscoinfacts.com/Coin/Detail/2953