Nobody can tell you anything without proper system info or other technical details like version of AE, items used, storage locations, comp settings and ultimately full error messages/ the collect files report. Yes, collect files is notoriously unreliably, but there's always a reason. Generalized assumptions and ranting don't help.
this is going to sound crazy, and I have tried this and it works, but don't move your mouse or use a pen tablet during the collect files process. there is a bug in AE that interrupts the collection process if new input is received, it seems. this has been noted on other threads regarding this issue. see here: AE CC Mac: After Effects Collect Files not collecting some files, including project!
so, hit enter on the keyboard, and don't touch anything until it's done.
I am experiencing the same problem. The "don't touch anything until it's done" sort of works, but with projects that have relatively large amounts of associate footage, it tends to hang up. This is really frustrating. Hey Adobe, any help with this? Updates coming soon with bug fixes, please?
Read this link:
In short, ensure you don't move the mouse once you have clicked 'Collect', hit 'Enter' Key instead.
Sounds bizarre, but it does work for me on Yosemite OS.