From what I have read on IMDB, the declaration was added after the film had already got very harsh criticism, from veterans, historians and some influential British people.
It is one thing to make something up. Another to misrepresent actual events, especially about things that happened in a war, that people still remember first- or second-hand.
I don't see how U-571 misrepresented anything. They never presented it as a true story. The fictional story wasn't a very close match for the real events. U-571 may have been the wrong movie to make, but that's a creative opinion. I don't think it deserved to get flak for misleading people.
There was no real Private Ryan either. But nobody gave Spielberg flak for lying. Nor did anybody say 'Private Ryan' was dishonoring the real people who inspired it. Why was it different with that movie?