The threefold repetition detection seems wrong when en passant is involved.
In the following example, the threefold repetition is said to occur after 6... Bc8 and the game is automatically drawn. However, the threefold repetition looks at the position, the possibility to capture en passant and castling status, so the threefold repetition occurs only after 8.. Bc8, not before. chess.com should automatically draw the game (if that is necessary at all, as in OTB there is no automatic draw with threefold repetition, but that is another question) after 8.. Bc8, not after 6... Bc8.
Example:
1. e4 Nf6
2. e5 d5 {Position arises, e5 can capture d5 en passant, repetition count #1}
3. Be2 Bd7
4. Bf1 Bc8 {Position arises, e5 cannot capture d5 en passant, so repetition count back to #1}
5. Bd3 Be6
6. Bf1 Bc8 {Position arises, e5 cannot capture d5 en passant, repetition count #2}
7. Bc4 Bf5
8. Bf1 Bc8 {Position arises, e5 cannot capture d5 en passant, repetition count #3}
Do you have a game where this happened? As far as I'm aware, the triple repetition code correctly accounts for that, though it is always possible a bug crept in.
Probably won't be in that big of a hurry to fix. 
I agree!