All of these were used for "reproof and doctrine" leading to a variety of heretical teachings (universal salvation, pre-existence of souls, a Smörgåsbord board of Christological heresies, Trinitarian heterodoxy, etc.) well into the late 3rd and early 4th century.
Maybe you don't mention it here because it's not directly relevant, but aren't there Christological and Trinitarian heresies that grew -- or at least were claimed to be found -- in the books finally declared canonical?
Yes, some of the Tirnitaruian and Chrisotlogical heresies do come from the canonical books as well, but many came form non-canonical, or the non-canonical books were used to "support" the heretical views found elsewhere.
The canonical books are full of ambiguities and textual variants that give "proof" to such views. Others are related to such factors as grammar. Take for instance the Jegovah's Witnesses' claim regarding John 1:1—it's all about one (nonexistent) indefinite article!