Early Installment Weirdness/Web Comics

The author of Gunnerkrigg Court admitted that the second chapter doesn't fit with the rest of the comic, because he was still figuring things out. Since it's popular with the fans, he's left it in place.
One of the first plot arcs in Questionable Content involves an aborted romance between Marten and Faye's coworker Sarah. Sarah vanished completely within the first 50 strips, as Faye and Dora became the female leads.
In Loserz, this meant that Ben didn't always act like he was struck with Tourette's Shitcock Syndrome when around girls. See here.
Xkcd initially wasn't even a webcomic, it was a site for Munroe to upload random sketches.
Keiki felt more like a Slice of Life comic in its early years, while the plotlines gradually became more outrageous.
Dan and Mab's Furry Adventures initially opened with it being quite clear that the characters were derived from the early MMO Furcadia, but then moved to being a more fleshed out world of its own, even if still retaining some of its old "MMO made real" elements -- Alexis' Banhammer became a magical greathammer, the Twinks become a "normal" organized crime gang, etc. And there are also other elements that linger a while before being more or less phased out -- for example, Lorenda was introduced having saved Jyrras from muggers by eating them, got evicted because she'd eaten her neighbors and then proceeds to eat several door-to-door salesmen. While she was admittedly self-proclaimed as preferring not to eat people, and this was a common source of friction with her mother, it hasn't been mentioned for hundreds of comics. In fact, neither has her much more predatory mother's tendency to eat people.
T and Gisele were hoping to syndicate Penny and Aggie at first, and early installments reflect this. There's much less sense of the passage of time, character development post-introduction ranges slow to absent, Charles and Finister are featured much more often, details about the setting are purposefully obscured to the point that the series could have taken place in Canada, and the Les Yay, aside from one bit of Love Letter Lunacy, is basically absent, even Sara in one strip being noticeably attracted to a boy; the Retcon of this makes it a plot point.
El Goonish Shive suffered from this with copious Fourth Wall Breaking, little or no backgrounds, poor story arc planning (some of which still poses a problem), and Tedd not having a permanently visible mouth.
Schlock Mercenary introduces several pieces of hardware as new or exceptional, then pretends that they were normal all along. The captain needs to be told what a fabricator ("Fabber") is, but later we see that they're widespread, important and something Tagon should probably know about. Even more odd is the fact the mercenary company doesn't start out wearing armor, either low or high profile, until they encounter a unit wearing some.
The first month of Homestuck consisted of John dicking around in his room and house and getting nothing done, and that was followed by a few months of mucking around with Sburb's ability to let them them to build and manipulate objects in each other's houses. Then things get more intense, to say the least. This can be chalked up to the fact that at that point, Homestuck was still driven by reader commands and they'd just come off the tail of the incredibly silly Problem Sleuth, so this is what people knew to do; the suggestion boxes were closed partway through and that's when the series is generally considered to have grown its very strange beard. A common symptom of this is people finding it difficult to get into Homestuck because of how long the first few months of dicking around is.
Even outside of Cerebus Syndrome and the Genre Shift, early Wapsi Square still had narration, which was absent from later strips as well as characterization that differed from what would come later.
Drowtales was originally set in the Forgotten Realms setting, and was a lot more explicit about sexuality, deliberately introducing Squicky details about the drow sex lives to wierd out the readers.