I think the main flaw of the movie is that it was trying too hard to convince us that the dystopian world was fake from the very start. For example, when Greg leaves his office and his wallet on his desk glitches. Greg wasn't there to see it so that was solely for the audience. Just like the multiplying background people or the van that Greg crushed with his mind.

It's clear by the end that those were all red herrings and the movie is about drug addiction and drug-induced psychosis. His prescription bottle read Hydrocodone, an opioid used for pain relief. On the phone he talked to his daughter about his fake injuries. He crushed his last two pills and snorted them off-screen before leaving his office. Isabel slips him something in his drink when they first meet, that's when his bender begins (along with the "powers"). From then on, Isabel and Greg seem to experience a drug-induced shared psychosis (aka folie à deux).

One way that could explain the "glitches in the Matrix" is if we assume that the audience is not an objective observer but either a third party in this shared psychosis or simply an extension of Greg's deluded imagination.