The NYT Crossword will typically clue “a little out of whack” with words such as “askew,” “off” or “uneven” depending on the puzzle's size. Many of the crossword clues are based on synonyms so it's helpful to use the crossword answers to help you narrow down the possibilities. One of the most popular fits for these types of clues is “Askew.”
A common guess for “little out of whack” in the NYT crossword would be “askew” or “awry,” depending on the letter count. NYT clues can be a bit tricky with wording, so crossing letters usually help narrow it down.