The hold time keeps running and nobody tells you.

This is the reason published hold times should be read as a ceiling rather than a plan. They are measured upright, unopened, at moderate ambient temperature. A customs hold breaks at least the last of those and often the first, and every opening for inspection costs hold time that cannot be recovered.

Two things reduce the damage. Build the margin against the delay you have not planned for rather than the journey you have, which in practice means sizing for considerably longer than the quoted transit. And make the expiry date visible: tell the receiving contact in writing what the hold time is and the date it runs out, so a delay becomes a decision somebody can act on rather than something discovered on arrival.

Correct documentation is the cheapest prevention available, since most holds are caused by an air waybill that does not say what it should.