Arc Fatigue: The comic had good pacing at the start of the series, but past the "Rescue Blossom" arc, things came to an rather annoying crawl, with the hiatuses not helping matters. For clarity, the comic's main plot started in 2004 and shaped up to be a standard heroes vs villains type of thing. At the time of this writing (2023), that conflict still hasn't really come to fruition nor what the villains are really planning.
Epileptic Trees: Bell. Is she a clone? A real Powerpuff Dr. X created? Someone who just has similar powers? Bleed originally envisioned her as a android, so that's also a possibility.
Bleedman draws the Powerpuff Girls grown up and with more realistic, anime style bodies. Then, a year later, Powerpuff Girls Z was announced.
Also with the Rowdyruff Boys, whose new appearance in the comic predated their return in the TV show.
And then came FusionFall, which seems to rip off Bleedman's style wholesale.
Jack's presence also predates Season 5's premise of still being in the future without having aged a bit.
Hype Backlash: Back in the day, the comic generated a lot of hype, but nowadays, there are a lot of factors that can cause this and Hype Aversion.
Moe: Bell. Drawn in a style much more reminiscent of the original Powerpuff Girls than the girls themselves and refers to GIR as "GIRLY".
Rescued from the Scrappy Heap: For 2018's April Fools Day joke, Bliss was put into the comic as the school's guidance counselor. Despite the negative reputation of the reboot, fan reaction to this was mostly positive, her design especially being praised. Some even hope she'll make other appearances outside the joke comic.
Ship-to-Ship Combat: While there are fans of Dexter and Blossom's relationship, there's a vocal portion of the PPGD fandom that prefers to ship Blossom with her Rowdyruff counterpart, Brick. The writer reinforcing that Dexter and Blossom were and always will be set as the Official Couple of the series didn't help quell the discourse either.
, so that's also a possibility.