So Google Chrome has recently stopped playing nicely with Little Snitch, mainly because there is an issue with Chrome that it creates a temp file to check for updates every X hours. Since its making a new temp file for some reason it sets off Little Snitch, which is quite annoying.
Entering the following code into your terminal will make it check once a week rather than every few hours:
defaults write com.google.Keystone.Agent checkInterval 604800
Hopefully one of the next version of Chrome they will address this, as it is very annoying having to click allow/deny every X hours.