Once RYG was teaching a shver Tosafot when one Talmid objected:
"But Rebbe, the M'harsha says ...."
To which RYG retorted "YOU don't understand the M'harsha"
And after a pregnant pause followed up with "and the M'HARSHA didn't understand Tosafot!"
At any rate - the salient point here As I Understand it is that RYG's primary fidelity was to achieving good p'shat, and it seems that often meant setting aside acharonim and analyzing Rishonim DIRECTLY. Perhaps in this case he objected mostly to this student distracting everyone's attention by citing a secondary source instead of focusing upon a primary one. As such the failure was probably mostly about not sweating out the Tosafot and taking a short-cut instead.
Summary: Since RYG's derech was Rishon-centric, therefore one should struggle with learning the Rishon, not in relying upon an intervening Acharon..