Yes. Stop the clock and call the TD.
This has occurred while I was a USCF Tournament Director in scholastic chess Swiss tournaments, especially in our unrated 5 min-blitz playoff games for trophies. I stopped the clock, had the players reset the pieces to both players agreement, then restarted the clock.
If one player was the only one at fault and did it twice, I gave a warning a 1 minute time penalty would go with the next one.
I was playing in an OTB tournament and my opponent and I were both down to about 1 minute on the clock with a 5 second increment. He had the better position. He was an experienced tournament player with a rating above 2000.
He makes a move, knocks over a couple of pieces in the process, punches my clock and does not replace the pieces---I was stunned, didn't know what to do, I replaced the pieces and made my move and punched the clock, but losing time on my clock while I was replacing pieces to their correct position. A couple of moves later, the same thing happened again---I lost the game on time---(I did have the worse position, but these kind of tactics really pissed me off and I think they may have been deliberate).
I should have called the TD, the first time that this happened and called for a judgement on the situation, but I was so involved in the game that I didn't think straight.
Has anything like this occured in your games?