How long or short does something have to be to qualify for a violation? Can a five second dialogue clip (like alerts) cause you to get a DMCA take-down?

There is no real precedent set for how long of a clip is “safe”. There have been lawsuits argued out in court over 8 notes that have been costly and time consuming for both parties involved. 

There is no “safe” amount of time or notes that will prevent a take-down notice from being issued. If you do not have the licenses to use the media in any portion, you are at risk of receiving a DMCA take-down

Read more about alerts here.