The top 5 things which cause me to mess up a timelapse sequence are:
1. Running out of battery power (camera or controller). 2. Running out of SD card memory capacity. 3. Incorrectly setting the camera, which usually happens when removing my camera from my rucksack and not checking all the settings before commencing the shoot. 4. Not fully spreading the tripod legs, which can lead to slight movement in high winds. Fortunately iMovie stabilization can usually solve it! 5. Dust particles or bugs on the lens. LR5 can remove them in a static sequence but if it’s a pan sequence (for example) it's much more difficult. Sometimes I have just deleted the offending frames!
I try to learn from my mistakes but it's a slow process!