During my undergrad research, producing a research paper took much longer than planned. While that was its own stressful ordeal, the delay unfortunately made my application suffer in three indirect ways:
1. By the time it was finished, I had to immediately drop everything and prepare for grad school applications (it was October and I hadn't even studied for the GRE or CSGRE yet!). Because of this and a lack of funding, I only had time to submit the paper to one very selective conference. The result is that I still have zero publications, when I could have feasibly gotten one or two.
2. Due to #1, I have been barely making deadlines for all the schools I have applied to so far. I was researching programs / groups so late in the game that I decided to apply to many at the last minute, meaning many of my mailed materials will be getting in late.
3. Also due to #1, I didn't leave myself any chances to retake the GRE tests, which it turned out I actually needed when I didn't do as well as I hoped. I got nervous and "bombed" the math portion of the GRE by running out of time. I spent too much time rigorously checking answers or struggling with the one or two questions I should have skipped. A score of 740 isn't awful, but competitive computer science students normally score higher, and I know I would do better if I retook it. Similarly, on the CSGRE I carefully took my time on the first half (feeling great about all my answers), then looked up at the clock and realized the test was almost over.