After a goalless first half, Germany were the first team to emerge for the start of the second period.
When the countdown clock on the scoreboard reached zero, the umpires re-started the match even though several British players were still making their way back onto the pitch.
Germany's Florian Fuchs then deflected the ball into an empty net.
Christophe Zeller and Moritz Furste increased Germany's lead before Britain's Ashley Jackson pulled one back for the hosts from the penalty spot.
"I think we had six or seven on the pitch and the umpires were told to start. It doesn't look great on anyone's part really," Jackson told the BBC.
Germany coach Markus Weise said: "To me it sounds like a typical hockey thing. I can't imagine other sports starting (like that).
"It's a very strange rule, probably provided by TV, that a game starts when the countdown is at zero. I don't want to be in a position without 11 players on the pitch and a game starting. It's a bit strange."
Great Britain coach Jason Lee insisted his team hadn't been time-wasting.
"It wasn't like we were four or five minutes late, we were 10 or 15 seconds late," Lee said. "But in hockey the ball goes so fast that you can't really get into position at that point.
"The changing rooms are a little bit further (away from the pitch) than what we'd expect."
Australia, the world's number one ranked men's side, beat India 3-0 thanks to goals from Russell Ford, Matt Gohdes and Luke Doerner.
In the women's tournament, Great Britain saw Alex Danson mark her 50th appearance with the only goal of the game in a 1-0 win over South Korea.
Argentina, the reigning world champions, defeated China 3-0.
