nothing is wrong with explorer IMO, you just transposed into position which can be reached via various move order. Try 1.e4
Nc6 2. Bb5 e5 , and you wil find a few games only. Then hit Nf3 and suddenly you will jump into Ruy Lopez with so many played games.
Seem's like a problem with inconsistent values, best to give example.
From this entry (1.c4 c6 2.Nf3 d5 3.e3), game explorer says that 19 games had the move 3 ... Bg4.
But after clicking into (3 ... Bg4), game explorer says that there were 171 games that had that position (171 = 95+58+9+7+2).
Am I misinterpreting the information, or is something incorrect with Game Explorer?