The explanation is clear after looking at the variant file for the WeMos D1 board definition:
static const uint8_t D0 = 3;
static const uint8_t D1 = 1;
static const uint8_t D2 = 16;
static const uint8_t D3 = 5;
static const uint8_t D4 = 4;
static const uint8_t D5 = 14;
static const uint8_t D6 = 12;
static const uint8_t D7 = 13;
static const uint8_t D8 = 0;
static const uint8_t D9 = 2;
static const uint8_t D10 = 15;
static const uint8_t D11 = 13;
static const uint8_t D12 = 12;
static const uint8_t D13 = 14;
static const uint8_t D14 = 4;
static const uint8_t D15 = 5;
In order to fill out the Uno-style form factor of the board, they connected some of the ESP8266's GPIO to multiple pins on the headers.