Wales trailed 19-14 with 20 seconds remaining on the clock and Samoa were gearing up to defend a scrum on their own five-metre line when Irish referee David Keane blew the final whistle.
Full-time on the IRB Sevens circuit is generally indicated by the official time-keeper, who sounds the hooter, and not by the referee's watch.
There was no guarantee Wales would have been able to turn over possession and score the match-winning try - but coach Dai Rees was disappointed they were not even given the chance.
"Every other game today was stopped on the hooter apart from this one. The referee told me he timed it on the watch. So why do we have external time-keepers?" said Rees.
"The referee missed a crossing incident which gave Kenya the momentum to go on and win that game, but you can accept those mistakes.
"This is protocol."
It is understood referee Keane apologised for the mix-up after the match but Wales were left to fight for third-tier honours in the Dubai shield competition.
Rees' men tackle Tunisia on Saturday.