Continuity Lock-Out: Despite each entry outside of the direct sequels meant to be mainly standalone, they keep building up on previous concepts, to the point where what's happening in Occultic;Nine and Anonymous;Code makes a lot more sense knowing the plot of Chaos;Head. With Steins;Gateovershadowing the first entry in popularity, a lot of players miss moments where the relation isn't trying to be subtle. Entries having a lot of Loose Canon spin-offs and manga creates even more references a casual player wouldn't understand.
Epileptic Trees: Realbooting is specifically a special ability in Chaos;Head to allow Gigalomaniacs physically manifest delusions through Visual Rebuilding and is the end goal of Norose Genichi and The Committee of 300 there. Because of how Visual Rebuilding is brought up in every game in one way or the other, it's commonly believed that every case of Psychic Powers in the franchise is an extension of how Gigalomaniacs work. Anonymous;Codetaking place Inside a Computer System fueled even more speculation, as "errors" and "hacking" are also mentioned alongside the supernatural phenomena across the series.
Porting Disaster: In addition to not having a very good official translation, the PC port of Robotics;Notes DaSH has its fair share of Game Breaking Bugs; the most notorious being crashes that may occur randomly when a cutscene ends.