England Under-21 manager Aidy Boothroyd felt play should have been stopped for a head injury before Germany's stoppage-time winner at the Vitality Stadium.
Defender Kyle Walker-Peters was down in the box when German defender Felix Uduokhai fired home a minute into added time.
The late goal condemned the Young Lions to a 2-1 defeat which ended their 18-match unbeaten run in their final scheduled fixture before Euro 2019.
Bournemouth striker Dominic Solanke, captaining the team on his home ground, looked to have earned Boothroyd's men a draw by cancelling out Mahmoud Dahoud's opener.
"It's disappointing to lose a run of games by an official that should have, in my opinion, blown for a free-kick," said Boothroyd.
"Kyle got caught, went down. To me, it's a head injury, it's Under-21s, it's a friendly – it stops.
"I'm disappointed, but we should not have given away the corner in the first place."
With senior team manager Gareth Southgate watching from the stands, an England side showing nine changes from the draw with Poland were fortunate to be level at the break following a dominant first-half display from the visitors.
After impressive Borussia Dortmund midfielder Dahoud fired home from the edge of the box in the 27th minute, Stefan Kuntz's side almost doubled their advantage when Luca Waldschmidt struck a post.
Boothroyd, whose team face France in their European Championship opener on June 18, believes there are lessons to be learned from the setback heading into the summer tournament in Italy and San Marino.
"It was tough. The first half, they were better than we were," he continued.
"The second half, we were miles better.
"If we are going to get beat, I'd rather we got beat now than in the Euros.
"We're all a bit hurt and disappointed but in my experience, sometimes a loss can be a really good thing."
Boothroyd has just over two months until he names his Euro 2019 squad.
Having lost Chelsea winger Callum Hudson-Odoi to the senior team during this international break, he admits there are a number of factors which could still affect his selection.
"It will get dictated by injuries, form, who Gareth wants, that always comes first," said Boothroyd.
"The amount of players I've been able to use and bring through... I think we'll be in a good place.
"I've learned an awful lot in the last two games. By the time the squad gets named on June 6, we'll be in a good position."
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