Not all broadcasts can be tracked effectively, this will be fixed soon
Kayn can fail to be tracked in recent VoDs, this is a result of Riot deciding to throw visual clarity out the window and adding his skins to the minimap :)
Vods with a lot of noise beforehand can slow down the program. Best input is a vod with only in-game footage, but avoiding pre-game highlights is ideal as the program may assume the game has started when it sees the highlight. This are features in place to alleviate this, but there is still a non-zero chance of it happening. If it happens, you can use the timestamp trick in Youtube URLs to skip ahead. For local videos? Currently no solution other than cutting your video manually.
VODs with single-team Fog of War (e.g. spectator replays focusing on one team) can fail when set to 'automatic' league.