How did Starfleet not know that warp drive was damaging space?

Or did they?

One of the Hekaran scientists presenting the damaging caused by warp drive.
(via Memory Alpha)

In the TNG episode "Forces of Nature", two alien scientists reveal that warp drive is damaging spacetime, with the area the episode takes place in being badly affected. This is demonstrated quite drastically after one of the scientists blows up her ship via warp core breach just to prove their point. After this, the Federation imposed a "speed limit" of warp five to mitigate damage.

Subspace rift caused by a warp core breach.
(via Memory Alpha)

What strikes me is that Starfleet or the Federation's scientists didn't know that warp drive could damage spacetime. Not once while they were developing newer, faster engines did anyone stumble upon evidence or even a notion that warp had such a negative effect?

(via Memory Alpha)

Or maybe they did and Starfleet buried it until a solution could be found. Maybe The Great Experiment (transwarp drive) was meant to be that solution and it's failure put them back at square one. The Intrepid-class's unusual warp nacelles may have been another attempt at fixing the problem. According to Memory Alpha, the unpublished tech manual for the first season of Star Trek: Voyager and the third edition of the Star Trek Encyclopedia both suggest that the Intrepid's "variable geometry pylons" eliminated the problem. The problem with that is that the Intrepids are the only ships in Starfleet service with VGPs - all the ships built after them (the Akira, Steamrunner, etc) all have conventional setups.

It's worth noting that in the non-canon Treklit, Starfleet appears to be actively fixing the problem by moving away from warp drive and towards quantum slipstream, but that's for another post.