It's usually not malicious, just disorganization. From a hiring manager's perspective, it's too easy for things to slip through the cracks. When the volume of candidates increases, it's hard to keep track of all the zip file submissions + individual repos while making sure the eng team reviews them all.
This is one of the problems my team is hoping to solve through software. So far, we're seeing teams working with us getting back to 100% of candidates (often with personalized feedback), with median times as fast as 1 day. I hope we can reduce the frequency of terrible take-home experiences.