problems were mostly with fanon rather than canon or continuity. Things like Spock being the first or only Vulcan in Starfleet. (disproved by the existence of a starship manned by Vulcans in "Immunity Syndrome" Or the NCC-1701 being the the first ship called Enterprise. (disproved by the ringship in TMP).
I like the ex-astris site, but mostly for its facts rather than its "editorials". They had a vested interest in their fanon version of the 22nd Century and the Romulan Wars, so I'm not surprised they would find fault with Enterprise. Must suck to have all your work rendered moot.