One letter and two letters are different clues
When a puzzle confirms two copies of the same letter, enter that letter twice in the contains field. A search for LL should require two Ls, while a search for L should require only one.
The word list changes sharply when the repeated letter is uncommon. Confirm the count before applying it because an extra copy can remove every otherwise plausible result.
Combine frequency with position
If one copy is fixed in a known position and another must appear elsewhere, keep the fixed copy in its slot and add one additional copy to the contains field. The two clue types then describe separate requirements.
Exclusions need the same care
Some puzzle feedback rules out an extra occurrence without ruling out the letter completely. In that situation, do not move the letter into the leave-out field. Preserve the confirmed copy and adjust only the uncertain clue.