Near the end of the R Roll dream, there is a shot where she's looking down at R Rockman, where she's missing her antennas.
There's a few occasions where Videoman's teeth are miscolored. While they're normally green, they're sometimes colored white in some shots.
The animators went through all the trouble to show Netto de-cross fusing, inserting new battle chips, and re-cross fusing. This means that any and every time the animators didn't show Netto/Enzan inserting chips before cross fusion (and they magically had them to use) is a goof (even more than it was before).
It never showed Netto and Enzan inserting battle chips before cross fusion... which happens quite often.
The concept of the Dimensional Converter sucking away navi hit points around it doesn't quite make sense. Never once has a DC sucked away a navi's life when they were near one in earlier episodes. For example, in episode #3, Netto (cross fused) was standing right beside a DC, beating it up and trying to break it. But he never began to lose his hit points.
It never showed Netto inserting battle chips before cross fusion. Usually, I let this slide... but in the way the sequence progressed, this is a goof.
The movie theatre had quite a few handy items just lying around... for example, how did Netto get a hold of a sledge-hammer to smash into the back entrance of the theatre? There was also a fire extinguisher and crowbar just lying around inside.
It seems strange how Rockman and Numberman perform the Soul Unison. There was absolutely no close relationship built up between the two before the occurrence. In fact, it seemed like it happened against Numberman's own will! It's also odd how Higure and Shuuko were the ones who were getting closer with each other before the unison -- if anything, THOSE two should have merged!
The device Dekao finds was designed for PET Advance's and created by Hikari Tadashi, Netto's grandfather. However, how could he have designed a device for a PET Advance that was created [by Enzan] after he died?
Netto thinks that the net navi saving him was Blues, when it was really Enzan in cross fusion mode. However, this brings up the question that I've wondered for a while. Why is it that only Darkloid navis are allowed to interact in dimensional areas? When one's activated, why doesn't Meiru, say, send Roll in to fight with Netto?
Enzan somehow managed to knock a dinosaur skeleton's head off and crush viruses by simply flinging a battle chip into it. Even if he somehow had the super-human strength to fling something THAT hard, the little piece of plastic that a battle chip is could never knock the head off.
The whole concept of the Star Lane Bowlin doesn't make any sense. How does a glove create a holographic bowling ball that copies a solid object, weight and all? Furthermore, how exactly is Bowlman able to destroy structures all over Japan from his cyber bowling alley? Is the entire world linked via the internet?
Why would a 23-year-old teacher start an onsen club with her 11-year-old student?
When Netto and Tamako battle at night, Netto is in his short towel again. However, as soon as the dimensional area appears, he's in his normal clothes. There's no way he could have changed clothes that quickly.
First time in Axess Cross Fusion isn't used in an episode (it's gonna show up a lot).
It doesn't make much sense how Flashman is able to hold a battle chip (the dark chip) in his hands and activate it... especially since he's still in the cyber world when he does it.
It's never quite explained why Netto needs to keep his identity as a Net Savior a secret. Perhaps the knowledge of his authority being out there would make him a prime target for attacks.
Chisao attends the field trip with Netto and Meiru... regardless that he's much younger than them and not in their class. However, in episode #54 of Rockman EXE, it's mentioned that Chisao attends Shin'nyussei Youchuen, a school for "super-smart kids," back in Ameroupe. Perhaps Chisao is in Netto's grade... but that doesn't explain why Tohru didn't go on the field trip.
Chisao visitting Japan at the moment seems pointless. He's Dekao's brother... Chisao lives in Ameroupe, but in Rockman EXE, Chisao visits Japan to spend time with his brother. However, in Axess, Dekao now lives in Jawaii... so it makes little sense to why Chisao is visitting Japan when his big brother isn't even there. It also seems odd that Chisao would be visitting in the middle of school. Does he attend a different school in Japan?