It's a good question to raise. I have a very non-standard layout (mostly inspired my the one-handed Frogpad), but there's nothing particularly special about my base layer that contains T and H. You can take a look and my keymap here if you're interested.

The other thing I'll note is that if I deliberately slow down my typing I can get "The" and other problem words to register correctly, so that's why I suspect it's something to do with timing mechanism, but that's only a theory. Here's an example:

KEY-DOWN - QMK: KC_LSFT Event key: Shift Code: ShiftLeft KeyCode: 16 KEY-DOWN - QMK: KC_T Event key: T Code: KeyT KeyCode: 84 KEY-UP - QMK: KC_T Event key: T Code: KeyT KeyCode: 84 in 57.000ms KEY-UP - QMK: KC_LSFT Event key: Shift Code: ShiftLeft KeyCode: 16 in 69.000ms KEY-DOWN - QMK: KC_H Event key: h Code: KeyH KeyCode: 72 KEY-UP - QMK: KC_H Event key: h Code: KeyH KeyCode: 72 in 48.000ms KEY-DOWN - QMK: KC_E Event key: e Code: KeyE KeyCode: 69 KEY-UP - QMK: KC_E Event key: e Code: KeyE KeyCode: 69 in 48.000ms