Yes, but this has much less of an impact than you might think. The transposition table is used to cache the evaluation and best move of previously looked at positions, which can speed up the search, by guiding it in the right direction. But probably the worst thing that can happen if it gets data from the wrong position is that it wastes some time looking at a bad move(also quite likely is that the move is illegal and it's just skipped), and then has to re-search the position because the result made no sense. Even if in theory it could lead to a misevaluation, ultimately Stockfish' move is decided by a vote between different search threads, so there would have to be a conspiracy between multiple threads as well. It's pretty unlikely they'll all see the same collision because they're set up to emergently end up in different parts of the search space. And the transposition table is constantly being updated.
