Regarding the specific position you mentioned, I'm not too sure of the answer, seems like a bug to me. In general, I do think it should give you the choice as to whether you want to include transpositions or not. Sometimes you may be interested in the position generally, other times only in a certain move order.
Someone help me understand this about Game Explorer..

It's all about move order.
If you enter 1 e3 e6
you will get very few games, if you now continue 2 e4 e5 there will be many thousands

After 1 e4 Nf6, 2.d4 is very rarely played as you can see, probably because it loses a pawn.
But play 2.d4 on the game board and the position arising after 2...d6 has occured many times, usually by the move order 1 e4 d6 2 d4 Nf6.
For another example, try playing 1. Nf3 Nf6 and you will see that 2. Ng1 has never been played. However play it on the game board and you will find over a million games, all of which have apparently had 2...Ng8 played in them!
It's the position after the move that the statistics are for, not the move itself.

...Obvioulsy it's possible to get to that position from a few other ways but they don't seem like they'd be very common ...
Try this move order.
http://www.chess.com/explorer/index.html?id=10051&ply=4
Edit: As indicated just before me in post #4

I cannot see Polar_Bear games via Explorer :
http://www.chess.com/echess/game?id=57291072
Can You ???
I was looking at understanding lines of Alekhine defense in the game explorer so I made the moves 1.e4 Nf6 and you are now given these games in the explorer:
http://www.chess.com/explorer/index.html?id=869&ply=2&black=0
Note how it only mentions 5 games were played from here where a player next moved 2. d4
Now if you put in 2. d4 you now end up with not 5 games but over 26 thousand from that position!:
http://www.chess.com/explorer/index.html?id=5383&ply=3&black=0
So I'm thinking ok maybe the explorer doesn't look at moves per se but just the position itself so I'm thinking maybe that position came up from 1.d4 Nf6 2. e4, so I started over and put in 1.d4 Nf6, but after doing so you're still then left with only 5 games were the next move for white was e4:
http://www.chess.com/explorer/index.html?id=19&ply=2&black=0
How did the position then after d4 or e4 on move 2 end up with over 26K games? I can't figure out what combination of moves led to there being over 26K games but only 5 and 5 based on the scenarios described above after 1d4 Nf6 2e4 or 1e4 Nf6 2.d4. Obvioulsy it's possible to get to that position from a few other ways but they don't seem like they'd be very common so I must be missing something?
Thanks for some clarification