The debates are regarding the underlying source documents that were used to assemble the gospels. E.g. Was there a Q? What was in Q? When was Q written? Who wrote Q? Why do the gospel stories have apparent contradictions? Who wrote those stories? Why? When? Based on what? How did they decide what to include and what to exclude? Do we even know what the original disciples thought of these stories?
There is so much we don't know about that first 100 years. At some point certain collected writings were deemed more authoritative, and there was a systematic purging of any disagreeable texts.
If you accept that parts of the gospel were written later in the first century based on stories that had been communicated verbally over long periods of time between different cities, cultures and languages... then the difference between the canon and the apocrypha becomes a little more blurry.
E.g. The Infancy Gospel of Thomas also date from the second century, and clearly shows wild stories were circulating verbally then being written down and accepted as canon by certain remote churches.
To paraphrase Ehrman & Fredriksen, you can argue that the stories in the gospels evolved and were selected largely to make certain theological points, or to counter the prevalent arguments against the religious movement.